In our book, Doubting Thomas, Dr. Mark Beliles and I show that the modern idea of Thomas Jefferson as a lifelong skeptic of Christianity does not fit the facts. After a few decades of a seeming good relationship between Jefferson and the church, during the campaign of 1800—when Jefferson ran for president against Federalist John Adams—some of the clergymen of New England began to criticize Jefferson for his faith or the alleged lack thereof. This marks the beginning of Jefferson and of some clergy (mostly opponents on a political basis) having a negative relationship—-not the previous positive one.
In contrast to his friendly relations with his local clergy, Jefferson made his first criticism of northeastern clergymen in a letter to James Madison, dated March 2, 1798, when he said that the New England states “are so priest-ridden, that nothing is to be expected from them, but the most bigoted passive obedience.”
State-churches still existed in New England and therefore priests still had favored status with government. But in contrast to this was Virginia which is illustrated by Jefferson’s reference to Albemarle County Baptist pastor William “Baptist Billy” Woods who Jefferson mentions in a letter on December 21, 1799: “our election [for Virginia House of Delegates] was yesterday. Woods carried it…” Woods, who corresponded and met with Jefferson on occassion, relinquished his ministerial license because the Virginia constitution barred clergymen from being elected to the assembly. Eight months later, Jefferson told Baptist clergyman Jeremiah Moore that he no longer supported this restriction.
The Federalist-aligned northern clergy, such as Congregationalists Rev. Timothy Dwight in Connecticut and Rev. Jedidiah Morse of Boston, began to question the faith of the presidential candidate Jefferson. Not a single clergyman in Virginia or any city south of New York ever opposed Jefferson on religious grounds while he was alive. Jefferson wrote to his friend, Bishop James Madison of Virginia at this time saying: “…Morse…& his ecclesiastical and monarchical associates [in the north] have been making such a hue and cry.” Bishop Madison replied giving his endorsement of Priestley as a philosopher and sharply criticized these Congregationalist leaders and especially Rev. Morse as “a blockhead.”