Russell Shorto in the New York Times Magazine:
There was a religious element to the American Revolution, which was so pronounced that you could just as well view the event in religious as in political terms. Many of the founders, especially the Southerners, were rebelling simultaneously against state-church oppression and English rule. The Connecticut Baptists saw Jefferson — an anti-Federalist who was bitterly opposed to the idea of establishment churches — as a friend. “Our constitution of government,” they wrote, “is not specific” with regard to a guarantee of religious freedoms that would protect them. Might the president offer some thoughts that, “like the radiant beams of the sun,” would shed light on the intent of the framers? In his reply, Jefferson said it was not the place of the president to involve himself in religion, and he expressed his belief that the First Amendment’s clauses — that the government must not establish a state religion (the so-called establishment clause) but also that it must ensure the free exercise of religion (what became known as the free-exercise clause) — meant, as far as he was concerned, that there was “a wall of separation between Church & State.”
This little episode, culminating in the famous “wall of separation” metaphor, highlights a number of points about teaching religion in American history. For one, it suggests — as the Christian activists maintain — how thoroughly the colonies were shot through with religion and how basic religion was to the cause of the revolutionaries.
More here.