I once spoke with my father in law about Jefferson's meaning under the First Amendment regarding establishment of religion, and one of the things that came up was Jefferson's letter to the Baptists regarding the "wall of separation" between church and state. My father in law insisted that this letter was written solely to quell the Baptists' concerns and not to stand for Jefferson's opinion on religion an church altogether.
I'm only a few pages into Jefferson and Madison on Separation of Church and State (edited by Lenni Brenner), but I came upon some notes Jefferson had written regarding religion: "No man has the power to let another prescribe his faith. Faith is not faith with[ou]t believing. No man can conform his faith to the dictates of another." (Jefferson and Madison on Separation of Church an State p. 26).
In addition, the Virginia Constitution, written with much input by Jefferson who included in his drafts that "all persons shall have full and free liberty of religious opinion; nor shall any be compelled to frequent or maintain any religious institution," had adopted the clause that "all Ministers of the Gospel of every Denomination be incapable of being elected Members of either House of Assembly or the Privy Council."
I'm only a few pages into this book, but I do clearly see the trend in Jefferson's writings towards keeping the clergy and the body politic separate. It's a shame that there are those on both the Religious Right and those opposed to the Religious Right who seek to simplify everything to one letter and injecting their opinions to the words written there.