Our book, Doubting Thomas, makes two simple points: 1) Jefferson was not a life-long skeptic, and 2) Jefferson did not believe in the idea that there should be no godly influence at work in the state. He certainly believed in the separation of the institution of the church from the institution of the state. But that is not the same as believing in the separation of God and government.
Here is a short section about when Jefferson was serving as vice president for a short while under John Adams. Presbyterian Rev. William Linn of New York wrote Vice-President Jefferson, now residing in Philadelphia much of the time, on May 25, 1797, on the subject of missions to Indians and included a pamphlet from the New York Missionary Society. Linn was one of the directors of the Society that sent its first missionary to the Chickasaws two years later in 1799. The editors of The Papers of Thomas Jefferson note that Jefferson and Linn often “…corresponded about their common interest in the American Indian tribes and their languages.” On February 5, 1798 Jefferson told Linn: “I should be very glad to [_______]…one of my [_______]…for the use of (your missionaries).” Although some words are illegible in the letter so that it is not clear what specifically he offered them, the main point is that he wanted to help their missionary work. And with previous donations to religious missionaries and later for Bible distribution to “the heathen” (their term for an unevangelized people group, but in this context, Indians), this cannot be dismissed as merely a secular motive.