On the contrary to the spirit of Maryland, Virginia armed itself and attacked her neighbor, declaring:

that no popish recusants should at any time hereafter exercize the place or places of secret councellors, register, comiss: surveyors or sheriffe, or any other publique place, but be utterly disabled for the same . . . it should not be lawfull under the penaltie aforesaid for any popish priest that shall hereafter arrive to remaine above five days after warning given for his departure by the Governour or commander of the place . . . (Ellis, 1956)

Massachusetts Bay followed suit, and instituted "anti-priests" laws:

This Court, taking into consideration the great warrs & combustions which are this day in Europe, & that the same are observed to be cheifly raysed & fomented by the secrit practises of those of the Jesuiticall order, for the prevention of like euills amongst o[ur]selues, its ordred, by the authorities of this Court, that no Jesuit or ecclesiasticall pson ordayned by ye authorite of the pope shall henceforth come w[ith]in o[ur] jurisdiction; & if any pson shall give any cause of suspision that he is one of such societie, he shalbe brought before some of the magists...to be tried & proceeded with by banish[ment] or otherwise . . . & if any such pson so banished shalbe taken the 2nd time w[ith]in this jurisdiction, he shall be vppon lawfull triall & conviction, be put to death . . . (Ellis, 1956)

In 1648, the "Toleration Act" was enacted to assure the inhabitants of Maryland it would not be the same for them.  The wording is as follows:

And I do further swear that I will not by myself or any other person, directly or indirectly trouble, molest, or discountenance any person whatever, professing to believe in Jesus Christ [remember there are only Catholics and Protestants], and in particular no Roman Catholic [they had fled persecution in England], for or in respect of religion, nor his or her free exercise thereof within the said province . . . nor will I make any difference of persons in conferring of offices, rewards or favors, for, or in respect to their said religion, but merely as I shall find them faithful and well deserving of his lordship and to the best of my understanding endowed with moral virtues and abilities; and if any other officer or persons whatsoever shall molest or disturb any person professing to believe in Jesus Christ, merely for, or in respect of hs or her religion, or the free exercise thereof, upon notice or complaint thereof made to him, I will apply my power and authority to relieve any person so molested or troubled, whereby he may have right done him. (Spalding, 1931)

This "oath" of the governor was later passed into "Act Concerning Religion":

Whereas, the enforcement of conscience in matters of religion hath frequently fallen out to be of dangerous consequences in these commonwealths where it has been practiced, and for the more quiet and peaceful government of this province, and the better to preserve mutual love and unity amongst the inhabitants, no person or persons whatever within this province or the islands, ports, harbors, creeks, or havens, therunto belonging, professing to believe in Jesus Christ, shall from henceforth be anyways troubled or molested, or dicountenanced, for, or in respect of his or her religion, nor in the free exercise thereof within this province or the islands thereunto belonging, nor any way compelled to the belief or exercise of any other religion, against his or her consent.

One may also say it contains the seeds of the civil religious freedom found in the Bill of Rights.  Many Puritans made use of this law to move to Maryland, and when Cromwell dissolved the Parliament in 1653, the Governor of Virginia found fit to replace Governor Stone of Maryland, who was Protestant, with Captain William Fuller, a Puritan.  Immediately the "Act of Toleration" was repealed and a law denying Catholics political power was enacted.
The persecution of Catholics did not end here.  The priests living quarters were ransacked, and the priests themselves became refugees.  Only with Cecil Calverts son taking over the Governorship in 1661 did some sort of toleration of Catholics exist in Maryland.  This was done by unenforcement of the existing laws forbidding the practice of Catholicism in a proprietorship that was set up specifically to give Catholics the ability to practice their religion. Priests, though outlawed, returned to administer to the Catholics in residence.  In 1690, with the transference of power in England to the House of Orange, Sir Lionel Copley was appointed Governor.  His first acts were to pass laws making the Protestant religion the official religion, with Anglicanism the established form to whom all had to pay taxes.  A law of 1699 demanded that everyone who took office deny the "doctrine of the Blessed Sacrament" and of 1716 forbidding anyone who held office could be present at any Catholic assembly or act of worship.  Many English Catholics chose to migrate to the Spanish possessions than live under such intolerance and persecution.
Massachusetts topped its 1647 laws by another Act on June 17, 1700.  Not heeding its mistake of 1692, when 20 innocent people were put to death during the Salem Witchcraft Trials, its officials and populace still saw satanic plots and chose Catholics as the propagators:

[Sect. 2] That all and every Jesuit, seminary priest, missionary or other spiritual or ecclesiastical person made or ordained by any authority, power or jurisdiction, derived, challenged or pretended, from the pope or see of Rome, or that shall profess himselfe or otherwise appear to be such by practising and teaching of others to say popish prayers, by celebrating masses, granting of absolutions, or using any other Romish ceremonies and rites of worship . . . after the tenth day of September aforesaid, shall be deemed and accounted an incendiary and disturber of the publick peace and safety, and an enemy of the true Christian religion, and shall be adjudged to suffer perpetual imprisonment; and if any person, being so sentenced and actually imprisoned, shall break prison and make his escape, and be afterwards re-taken, he shall be punished with death. (Ellis, 1956)

The Colonists of New York entreated the Indians in 1701 to dismiss their French Priests, to whom the Indians replied:

You are too late in undertaking to instruct us in the prayer after all the many years we have been known you.  The Frenchman was wiser than you.  As soon as we knew him, he taught us how to pray to God properly, and now we pray better than you. (Shea, 1886)

This persecution was the same in all the other Colonies except Pennsylvania.  New Jersey and Rhode Island gave religious freedom to all "except papists." (Shea, 1886)  The first priest to die at the hands of the English Colonists would be Father Rale, who was slain at Norridgewock in 1724. (Shea, 1905) Massachusetts had sent several expeditions to destroy the mission stations, and the Governor, as he claimed Maine to be part of the Massachusetts Colony, sent a letter to Father Rale forbidding him to preach or even remain.  With a force of 230 men, Colonel Westbrook, in the autumn of 1723, destroyed Father Rales mission and carried off his possessions.  The next year, Colonel Moulton surprised the village, killing Father Rale and many of the Indians.  The remaining Indians departed for Canada.
In the displacement of the Catholic Acadians by the English, the attitude of the Colonists was also apparent in their reception of these "ignorant Catholics" (Shea, 1886).   The two thousand who landed in Massachusetts were not permitted the public exercise of their religion with a Catholic priest.  Those sent to New York suffered even worse. The adults were employed as their children were sent away to become "useful, good subjects."  Requests from other French Colonists to allow the Acadians to emigrate were denied.  In Maryland, the Acadians were not allowed to lodge with Catholic families. Malnourished, wearing rags, and suffering illnesses most died.  Those who lived made every attempt to reach Spanish or French territory. Only Pennsylvania provided some relief to its influx of Acadians. Small as this number was and despite a cry of possible invasion by "Catholics", the inhabitants soon recognized their fear was unfounded and the Acadians were administered by the Catholic priests who were already administering to the English and German Catholics.
While the English Colonies may have been malevolent toward Catholicism, the Catholic Church did flourish in other parts of the future United States.  Florida, Alabama, and Louisiana became centers of Spanish Catholicism. The regions along the Saint Lawrence and the Great Lakes continued to be centers of French Catholicism. Father Eusebio Kino was active in present Arizona in the first decades of the 1700s.  Texas and New Mexico were well established territories of Spain.  By 1769, California was being missionized by Padre Junipero Serra.
The history of the colonization of Maryland should have been a lesson to Catholics in America. The Catholics from England were fleeing religious persecution. They knew other persons were fleeing England for the same cause, persecution for not being Anglicans, members of the Church of England. Still, the persecution continued in the Colonies for Catholics, but it was from those very ones who were fleeing for the same reason, the Puritans. In spite of themselves suffering under the Anglicans, the Puritans were even more tyrannical than their Persecutors. Opening Maryland to civil tolerance of other religions was certainly a protective act, since Catholics were in a minority, yet it only allowed the Puritans and then the Anglicans to re-institute anti-Catholic Laws. Persecution of Catholics is nothing new, and the English regimes had been exceptional in their application of murdering and annihilating Catholics since Henry VIIIs schism that could only be compared to Nero and Diocletian. Arriving in 1634 under the assurance of being free to live as Catholics, already in 1653, nineteen years later, the Catholics found themselves in the same predicament that drove them from their homeland in the first place: laws against their publicly living and professing their Catholic Faith.
Textbooks about the history of the United States seem to have a disconnect between events happening in England and on the Continent. This may be for attempting to insinuate that English events had no impact on the colonists and therefore the independence of the colonists from anything happening on the British Isles. Yet, when Oliver Cromwell set up the Commonwealth of England, it meant anything Catholic was game for hatred and obliteration. The invasion of Ireland and the deportation of over 50,000 Irish Catholics as slaves sent to the British Colonies to work the plantations is never mentioned. The armies of Cromwell wiped out entire villages in Ireland and set up British domination. On the Continent, it meant that Maryland was invaded by the Virginians who joined the Puritans in displacing the Maryland governor along with the Act of Tolerance. Catholics were put to death and priests were forced to flee. With the accession of James II, some calm was restored until once again the English Isles saw the overthrow of another monarch sympathetic to Catholics. Then again persecution of Catholic colonists took vogue, and the Catholics were confined to the penal laws imposed on them by the new Protestant Monarchs sworn to deny Catholics any civil rights. This “Glorious Revolution” kept the hatred of Protestant English toward Catholicism enkindled for another hundred-forty years, until in 1829 the last of the penal laws were repealed. Under such oppressive persecution, Catholics in the colonies sought some civil freedom to practice their faith. They found this answer in the American Revolution.

The experience of James II and his overthrow taught Catholics in England and in the colonies that the only means to obtain some freedom was not to seek a restoration of Catholicism in what was once Catholic England, but rather a simple civil freedom that allowed Catholics to practice their faith without penalization or fear of losing their property and lives.
Taking a step back in history, it was in the year 312, on October 28, when Constantine defeated the forces of Maxentius, that started the beginning of the end of open persecution of Christians by the Roman State. Constantine, with an inferior army, easily prevailed by the assistance of Gods intervention. Attributing the decision to a vision in which he saw a cross in the sky and the words, In hoc signum vinces—In this sign you shall conquer, Constantine had his legions mark their shields with the sign of the Cross. In gratitude he drew up The Edict of Milan of 313 that guaranteed tolerance of Christianity (Catholicism) and the right of Christians to practice their faith without molestation:

Therefore, [in your devotion it] should know that it has pleased us to remove all conditions whatsoever, which were in the rescripts formerly given to you officially, concerning the Christians and now any one of these who wishes to observe Christian religion may do so freely and openly, without molestation. We thought it fit to commend these things most fully to your care that you may know that we have given to those Christians free and unrestricted opportunity of religious worship. When you see that this has been granted to them by us, [your devotion] will know that we have also conceded to other religions the right of open and free observance of their worship for the sake of the peace of our times, that each one may have the free opportunity to worship as he pleases; this regulation is made that we may not seem to detract from any dignity or any religion. [From Lactantius, De Mort. Pers., ch. 48. opera, ed. O. F. Fritzsche, II, p 288 sq. (Bibl Patr. Ecc. Lat. XI). Translated in University of Pennsylvania. Dept. of History: Translations and Reprints from the Original Sources of European history, (Philadelphia, University of Pennsylvania Press [1897?-1907?]), Vol 4:, 1, pp. 28-30.]

Constantines son, Constantius, was intolerant of paganism and began the reversal of religious tolerance that would soon be encoded in the Theodosian decretals, or Codex Theodosianus. Theodosius, though not strictly enforcing his decrees upon individuals, nevertheless closed all temples and united the Roman Empire under the Christian religion:

C. Th.XVI.i.2: We desire that all the people under the rule of our clemency should live by that religion which divine Peter the apostle is said to have given to the Romans, and which it is evident that Pope Damasus and Peter, bishop of Alexandria, a man of apostolic sanctity, followed; that is that we should believe in the one deity of Father, Son, and Holy Spirit with equal majesty and in the Holy Trinity according to the apostolic teaching and the authority of the gospel. Gratian, Valentinian and Theodosius Augusti. [Oliver J. Thatcher, ed., The Library of Original Sources (Milwaukee: University Research Extension Co., 1907), Vol. IV: The Early Medieval World, pp. 69-71.]

The tone of the Theodosian decree was not one of intolerance, but by the Protestant Reformation it was interpreted as cujus regio, ejus religio—turning once Catholic states into Protestant dominions and intolerance as the only option for Catholics was to move to a Catholic state. Where Catholic rulers applied this Augsburg compromise (1555) of Charles V, the Protestants—as their name suggests—protested and demanded equality. This brought on the Religious Wars of the 16th and 17th centuries that left much of Continental Europe in ruin. Most of those migrating to the Americas did so to avoid the Religious Wars, seeking to practice their faith without interference. Yet, as seen above, the persecution continued even in the English Colonies.
In England, taking the step even further, Henry VIII declared himself Head of the Church of England. Loyal subjects were obliged to become Anglicans or face treason. When his illegitimate daughter, Elizabeth, was placed on the throne as queen, the persecution was so intense that Catholics were hunted like animals and cruelly tortured. Pope St. Pius V excommunicated Elizabeth and sent a letter, Regnans in Excelsis, dated 27th April, 1570, deposing her as queen:

We do out of the fullness of our apostolic power declare the foresaid Elizabeth to be a heretic and favourer of heretics, and her adherents in the matters aforesaid to have incurred the sentence of excommunication and to be cut off from the unity of the body of Christ.
And moreover (we declare) her to be deprived of her pretended title to the aforesaid crown and of all lordship, dignity and privilege whatsoever.
And also (declare) the nobles, subjects and people of the said realm and all others who have in any way sworn oaths to her, to be forever absolved from such an oath and from any duty arising from lordshop. fealty and obedience; and we do, by authority of these presents , so absolve them and so deprive the same Elizabeth of her pretended title to the crown and all other the abovesaid matters. We charge and command all and singular the nobles, subjects, peoples and others afore said that they do not dare obey her orders, mandates and laws. Those who shall act to the contrary we include in the like sentence of excommunication. (27 April, 1570)

But it seemingly did more harm, enflaming the Protestant English to rid England of all popery and add even more penalties upon Catholics. Unfortunately the Pope was not able to rally enough faithful Catholics, who now found themselves a minority in England, to oppose this most iniquitous Ruler. She had Parliament enact further Penal Laws against Catholics, which are directed against the Popes letter. Edwin Burton summarizes them as follows:

13 Eliz. c.1, which, among other enactments, made it high treason to affirm that the queen ought not to enjoy the Crown, or to declare her to be a heretic or schismatic, and 13 Eliz. c. 2, which made it high treason to put into effect any papal Bull of absolution, to absolve or reconcile any person to the Catholic Church, or to be so absolved or reconciled, or to procure or publish any papal Bull or writing whatsoever. [Burton, E. (1911). Penal Laws. In The Catholic Encyclopedia. New York: Robert Appleton Company.]

The saintly Popes intervention also found little support among the Catholic faithful, for the letter of deposition saw an overt rejection of its force even by Catholics of the Pope’s right to interfere in the political sphere. This is obvious in reading the life of Blessed Edmund Campion, where he unabashedly continues to refer to Elizabeth as my Queen.
It was in this atmosphere of renewed religious persecution, not seen since the Roman persecutions, which Catholics in the English Colonies would reflect and acknowledge with their fellow American Colonists that civil freedom of Religion would need to be established if they were to co-exist without persecution by the State or a tyrannical majority.
As is known, the states that succumbed to Protestant Rulers, endured extreme tyranny, whether from under Zwingli and Calvin and Cromwell as religious zealots become rulers, or from Frederic of Saxony and Henry VIII and Elizabeth I becoming heads of their national Church. The over 250 years between the beginning of the Protestant Reformation and the American War for Independence cannot be deleted with all the suffering simple Catholics and Protestants had to endure and the acceptance that for many the journey to the American Continent was for freedom to live their religion—not from Catholic Rulers, but Protestant. This is why later the founders will always stress the importance of religion while demanding that state and church be separated. Of course, this view must also be examined through the Catholic faith and it will be as another topic.
Setting aside the various causes that, summed up, would bring about the American Revolution, what will be considered is the relationship and involvement of Catholics within the thirteen colonies joining with a determination to obtain the freedom to live their Catholic faith.  In the English colonies, Catholics numbered less than 30,000 of the 2.5 million inhabitants by 1776. Catholics, though definitely on the outside margins of colonial society, would become the deciding factor to winning independence.
When addressing the issue of relationships between the French Catholics in Canada and the Revolutionary forces of the United States, it is necessary to keep the above treatment of Catholics in view.  What one does see is the cooperation of English Catholics and German Catholics in participating with the Revolutionary Forces.  Still, not without a struggle to obtain their own religious liberty within the Revolution.  This we can sense in the events surrounding this specific period of history.
As the Continental Congress first convened, one of its first Resolutions was against the granting of Religious Freedom to Catholics in Canada:

September 17, 1774:
"That the late act of parliament for establishing the Roman Catholic religion and the French Laws in that extensive country, now called Canada, is dangerous in an extreme degree to the Protestant religion and to the civil rights and liberties of all America; and, therefore, as men and Protestant Christians, we are indispensably obliged to take all proper measures for our security." (Ellis, 1956).

John Jay spear-headed tirades against Catholics in New York.  Catholics were labeled as Tories and many were driven out.  But this did not prevent Catholics from continuing to swell the ranks of the Continental Army and in obtaining support of the Catholic Canadians.  In a direct reversal of the Resolution of September 17, 1774, the Continental Congress wrote on May 29, 1775, to the Canadians:

Since the conclusion of the late war, we have been happy in considering you as fellow-subjects, and from the commencement of the present plan for subjugating the continent, we have viewed you as fellow-sufferers with us. As we were both entitled by the bounty of an indulgent creator to freedom, and being both devoted by the cruel edicts of a despotic administration, to common ruin, we perceived the fate of the protestant and catholic colonies to be strongly linked together, and therefore invited you to join with us in resolving to be free, and in rejecting, with distain, the fetters of slavery, however artfully polished." (Ford, 1905).

This went on with a promise of religious freedom for all. Such was the support and influx of Catholics and the realization by George Washington of the needed support of Catholics that he forbade the Guy Fawkes Day, in which an effigy of the pope was burned.  It was a turn in American history:

General Orders
Head Quarters, Cambridge, November 5, 1775.
As the Commander in Chief has been apprized of a design formed for the observance of that ridiculous and childish custom of burning the Effigy of the pope—He cannot help expressing his surprise that there should be Officers and Soldiers in this army so void of common sense, as not to see the impropriety of such a step at this Juncture; at a Time when we are solliciting, and have really obtained, the friendship and alliance of the people of Canada, whom we ought to consider as Brethren embarked in the same Cause.  The defence of the general Liberty of America: At such a juncture, and in such Circumstances, to be insulting their Religion, is so monstrous, as not to be suffered or excused; indeed instead of offering the most remote insult, it is our duty to address public thanks to these our Brethren, as to them we are so much indebted for every late happy Success over the common Enemy in Canada. (Ellis, 1956)

By February 17, 1776, the Continental Congress resolved to send the Catholic priest, John Carroll, to the Canadians to deliver their assurances.  On March 20, 1776, it issued the following instructions:

You are, with all convenient despatch, to repair to Canada, and make known to all the people of that country, the wishes and intentions of the Congress with respect to them...
...[T]hat the people of Canada may set up such a form of government, as will most likely, in their judgment, to produce their happiness...
...[T]hat we hold sacred the rights of conscience, and may promise the whole people , solemnly in our name, the free and undisturbed exercise of their religion; and, to the clergy, the full, perfect, and peaceable possession and enjoyment of all their estates; that the government of everything relating to their religion  and clergy, shall be left entirely in the hands of the good people of that province, and such legislature they shall constitute; Provided, however, that all other denominations of Christians be equally entitled to hold offices, and enjoy civil privileges, and the free exerrcise of their religion, and be totally exempt from the payment of any tythes or taxes for the support of any religion. (Ford, 1906)

At this turn in history several States changed their laws regarding religion.  On September 28, 1776, Pennsylvania adopted a Declaration of Rights which included, "That all men have a natural and inalienable right to worship Almighty God according to the dictates of their own consciences and understanding...." (Ellis, 1956).  Maryland followed suit on November 11, 1776.  New York changed its constitution to include "free exercise and enjoyment of religious profession."  

Charles Carroll took his seat in Congress at Philadelphia as a delegate from Maryland, John Barry came forward to win fame as one of the chief founders of the American navy, Stephen Moylan joined Washington`s staff as muster master-general, Daniel Carroll was named a member of Congress from Maryland, and Thomas FitzSimons represented Pennsylvania. Moreover, after the alliance with France was signed in February, 1778, units of the French fleet began to dock at Philadelphia, each with its Catholic chaplain. Soon, too, the first French minister, Conrad Alexandre Gerard, became one of the leading personalities in the capital city, and when he sent out invitations in 1779 to a Te Deum in St. Marys Church to mark the third anniversary of American independence and two years later to commemorate the victory of Yorktown, members of Congress found it expedient to be present. It had now become unthinkable to offer public or official slights to Catholics with France so close and powerful an ally. (Ellis, 1955)

Catholics were to be found  supporting both sides of the war effort, but the with George Washington promising liberty, the majority were to cast their lot with the Revolutionary Army, where, unlike the English forces, they would rise in position such for example: Captains Joshua Barney and John Barry, who were successful naval commanders; Colonel John Fitzgerald, a trusted aide and private secretary to General George Washington; Colonel Thomas Moore of one of the Philadelphia regiments; and Major John Doyle, who led a group of elite riflemen.
Besides these, there were the French soldiers under Lafayette – who were accompanied by Catholic Chaplains and Father Pierre Gibault, Vicar General of Illinois, who aided in the conquest of the Northwest.
The result of the support of Catholics in the cause of the American Revolution is to be found in the Constitution of the United States of America, adopted September 17, 1787. Here one reads:
[VI.] No religious Test shall ever be required as a Qualification to any Office of public Trust under the United States.  Finally, in the Bill of Rights (Amendments): [1] Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof.

Understanding that the United States is not a Catholic Nation, but was originally established as a Freemasonic Republic, based on the so-called principles of the Age of Enlightenment that was propagated within by Masonic Secret Societies. On Continental Europe these Lodges conspired to overthrow Catholic Monarchies and the power of the Catholic Church — as the French Revolution gives witness and with the consequential overthrow of all Catholic Monarchies throughout Europe. In the English Colonies, the Lodges—members of which called themselves Sons of Liberty — conspired to overthrow English rule and establish a Freemasonic Republic [The English did not have a Catholic Monarch and the Catholic Church was already forbidden]. Though some were extremely radical and anti-Catholic, such as Thomas Paine and Ethan Allen, most were simply seeking liberation from the tyrannical domination that England imposed on its colonists.
The cooperation of all colonists who participated in the Revolutionary War, which extended from 1774 (First Continental Congress) to 1783 (Signing of Paris Peace Treaty)—though military fighting was only between 1775-1781—was obtained by guaranteeing each colonist and colony what they demanded—freedom: from tyranny, from taxation, from established religion, from slavery. The Articles of Confederation attempted to place the power of decision in the hands of each individual state, but it was soon apparent that the states were not capable of incorporating or sustaining those promises or cooperating to even meet the needs of a United States—rather each State sought its own advantages without any executive or judicial authority to intervene and no ability to raise taxes to pay the soldiers who were serving in the Revolutionary War.
The citizens, with newly obtained liberty, did not want to pay taxes [cf. Shays Rebellion] or give up slavery [in fact, freedom for the African bondman became more unobtainable than before the Revolution—resentment being high toward them among the European Americans in that many African bondmen supported the British, being promised freedom (cf. Lord Dunmores Proclamation of November 7, 1775: And I hereby further declare all indented servants, Negroes, or others (appertaining to Rebels) free, that are able and willing to bear arms, they joining His Majestys Troops, as soon as may be, for the more speedily reducing the Colony to a proper sense of their duty, to this Majestys crown and dignity.)]. It was therefore obvious that certain promises could not be granted if the United States of America was to survive. But certain promises were also guaranteed to remain untouched. One such guarantee was the civil freedom of Religion (which meant freedom from imposed religion).
Even though some States struggled with Freedom of Religion, it was not because they did want freedom from Religion, it was defining what is “Freedom of Religion”. Thomas Jefferson is used by those trying to free the United States of America from Religion, when in fact he was opposed of the State interfering with religion in any way, so much so that he wrote The Virginia Statute of Religious Freedom soon after the Declaration of Independence. It was introduced on June 12, 1779, but it did not pass. James Madison, without whom it probably would never have been enacted, engineered its passage in the General Assembly in 1786, before the United States Constitution granted Religious Freedom in the Bill of Rights. James Madison is also one of the Framers for the United States Constitution and one would be safe to assume Madison understood Freedom of Religion in the context of this Virginia Statute which states:

Be it enacted by General Assembly that no man shall be compelled to frequent or support any religious worship, place, or ministry whatsoever, nor shall be enforced, restrained, molested, or burthened in his body or goods, nor shall otherwise suffer on account of his religious opinions or belief, but that all men shall be free to profess, and by argument to maintain, their opinions in matters of Religion, and that the same shall in no wise diminish, enlarge or affect their civil capacities. And though we well know that this Assembly elected by the people for the ordinary purposes of Legislation only, have no power to restrain the acts of succeeding Assemblies constituted with powers equal to our own, and that therefore to declare this act irrevocable would be of no effect in law; yet we are free to declare, and do declare that the rights hereby asserted, are of the natural rights of mankind, and that if any act shall be hereafter passed to repeal the present or to narrow its operation, such act will be an infringement of natural right.

And which Thomas Jefferson, as President, only reiterated in his letter to the Danbury Baptists of January 1, 1801:

… I contemplate with sovereign reverence that act of the whole American people which declared that their legislature should "make no law respecting an establishment of religion, or prohibiting the free exercise thereof," thus building a wall of separation between Church and State. Adhering to this expression of the supreme will of the nation in behalf of the rights of conscience, I shall see with sincere satisfaction the progress of those sentiments which tend to restore to man all his natural rights, convinced he has no natural right in opposition to his social duties.

Understood in the sense as stressed by these documents, the Government cannot decide issues of Religion, which is a natural right as “life, liberty, and the pursuit of happiness” were spelled out in the Declaration of Independence.
The attitude of individual states and individuals did not necessarily express the theoretical in practical application; but George Washington, in thanking Catholics for their support, guaranteed them and all protection of their Religious Freedom:

[March 15], 1790

Gentlemen:

While I now receive with much satisfaction your congratulations on my being called, by an unanimous vote, to the first station in my country; I cannot but duly notice your politeness in offering an apology for the unavoidable delay. As that delay has given you an opportunity of realizing, instead of anticipating, the benefits of the general government, you will do me the justice to believe, that your testimony of the increase of the public prosperity, enhances the pleasure which I should otherwise have experienced from your affectionate address.

I feel that my conduct, in war and in peace, has met with more general approbation than could reasonably have been expected and I find myself disposed to consider that fortunate circumstance, in a great degree, resulting from the able support and extraordinary candour of my fellow-citizens of all denominations.
The prospect of national prosperity now before us is truly animating, and ought to excite the exertions of all good men to establish and secure the happiness of their country, in the permanent duration of its freedom and independence. America, under the smiles of a Divine Providence, the protection of a good government, and the cultivation of manners, morals, and piety, cannot fail of attaining an uncommon degree of eminence, in literature, commerce, agriculture, improvements at home and respectability abroad.
As mankind become more liberal they will be more apt to allow that all those who conduct themselves as worthy members of the community are equally entitled to the protection of civil government. I hope ever to see America among the foremost nations in examples of justice and liberality. And I presume that your fellow-citizens will not forget the patriotic part which you took in the accomplishment of their Revolution, and the establishment of their government; or the important assistance which they received from a nation in which the Roman Catholic faith is professed.
I thank you, gentlemen, for your kind concern for me. While my life and my health shall continue, in whatever situation I may be, it shall be my constant endeavour to justify the favourable sentiments which you are pleased to express of my conduct. And may the members of your society in America, animated alone by the pure spirit of Christianity, and still conducting themselves as the faithful subjects of our free government, enjoy every temporal and spiritual felicity.

G. Washington

One of the most anti-Catholic States, Massachusetts, finally amended its constitution in 1780. This civil freedom, as Thomas Jefferson expressed it, the “wall of separation”, has never been questioned or opposed; if anything, perhaps, previously it was the government siding on the issue of religion more than opposing its influence.


REFERENCES and BIBLIOGRAPHY

Barry, Coleman J. O.S.B. (1953). The Catholic Church and German Americans.  The Bruce Publishing Company.  Milwaukee.

Ellis, John Tracy. (1955). American Catholicism. The University of Chicago Press. Chicago.

Ellis, John Tracy. (1956). Documents of American Catholic History.  The Bruce Publishing
Company.  Milwaukee.

Ellis, John Tracy. (1962) Documents of American Catholic History 2nd Ed., The Bruce Publishing Company, Milwaukee.

Ford, Worthington C. (1905). Journals of the Continental Congress 1774-1789. Vol. II. Library of Congress. Washington.

Ford, Worthington C. (1906). Journals of the Continental Congress 1774-1789. Vol. IV. Library of Congress. Washington.

Melville, Annabelle M. (1955). John Carroll of Baltimore. Charles Scribners Sons. New York.

Murphy, Thomas J. (2001). Jesuit Slaveholding in Maryland, 1717-1838, New York, Routledge,

OBrien Hanley, Thomas. (1976) The John Carroll Papers Volume I-1755-1791. University of Notre Dame, IN.

OBrien Hanley, Thomas. (1976) The John Carroll Papers Volume II-1792-1806. University of Notre Dame, IN.

Quigley, Thomas J. & Mary Denis Donovan. (1960). The Christian Citizen.  Mentzer, Bush and Company.  Chicago.

Shea, John G. (1905). Our Church and Country. The Catholic Historical League of America. New Haven, CT.

Shea, John G. (1886). History of the Catholic Church in America (Vol. I). D. H. McBride & Co. Akron, OH.

Spalding, Henry S. (1931). Catholic Colonial Maryland. The Bruce Publishing Company. Milwaukee