Understanding What Drove Political-Theological Notions of Liberty of Conscience During The American Founding

Catholics Persecuted Protestants; Protestants Persecuted Catholics; and Protestants Persecuted One Another.

The different sects disagreed with one another. But it went beyond mere disagreement. America's founders were acutely aware of the history of religious conflict that occurred after the Protestant reformation. The "political-theological problem," recent in their historical memory, that America's founders wished to transcend. This needs to be stressed to understand how America's founders understood the notion of "liberty of conscience" which they viewed as the most "unalienable" of rights. 

Here is George Washington reflecting on this dynamic:

I was in hopes that the enlightened & liberal policy which has marked the present age would at least have reconciled Christians of every denomination so far that we should never again see their religious disputes carried to such a pitch as to endanger the peace of Society.

There is contention over whose ideology is responsible for the American founding. As I see it, the ideological origins of the American founding came from disparate streams that formed an amalgam. Christianity, or Protestant Christianity, was one of four or five chief ideological sources (see Bernard Bailyn). Though, the Protestant Christian component was extremely "pluralistic" for lack of a better term, in a sectarian sense of the term (pluralities of sects). 

Mark David Hall and others argue that reformed/Calvinism predominated. That may be true. However, there were plenty of other sects who not only fought for their "place at the table," but did so with a strong distrust of Calvinists, especially of the Presbyterian bent. This is John Adams writing on how he regretted his recommendation for a National Fast as President because of Presbyterian distrust!

The National Fast, recommended by me turned me out of office. It was connected with the general assembly of the Presbyterian Church, which I had no concern in. That assembly has allarmed and alienated Quakers, Anabaptists, Mennonists, Moravians, Swedenborgians, Methodists, Catholicks, protestant Episcopalians, Arians, Socinians, Armenians, & & &, Atheists and Deists might be added. A general Suspicon prevailed that the Presbyterian Church was ambitious and aimed at an Establishment of a National Church. I was represented as a Presbyterian and at the head of this political and ecclesiastical Project. The secret whisper ran through them “Let us have Jefferson, Madison, Burr, any body, whether they be Philosophers, Deists, or even Atheists, rather than a Presbyterian President.” This principle is at the bottom of the unpopularity of national Fasts and Thanksgivings. Nothing is more dreaded than the National Government meddling with Religion.

Finally, much has been made about Thomas Jefferson's letter to the Danbury Baptists wherein he invokes the term "separation of church and state." Much ink has been spilt on "the context" of what was meant by Jefferson's "Wall of Separation" and the implications thereof. Here is something to keep in mind: The "context" of the letter was a "complaint" about a particular religious sect who had control over Connecticut's then religious establishment -- the reformed/Calvinistic Congregational Church. Both Jefferson and the Danbury Baptists wanted to be "separate" from THEM. That's against whom their "wall" was directed.