During the election of 1800, there was a great deal of acrimony. Some of the charges against Thomas Jefferson, alleging that he wasn’t a Christian were hurled at him at that time—because of political reasons. We address this in our book, Doubting Thomas. It’s hard to imagine muckraking by politicians running for offices. But there it is.
For example, there was an opposition piece called “The Voice of Warning, to Christians, on the Ensuing Election of a President of the United States,” by Rev. John M. Mason of New York (who claimed Jefferson was a “confirmed infidel”). A decade later Jefferson said: “I do not know Dr. Mason personally, but by character well. He is the most red hot federalist, famous, or rather infamous for the lying & slandering which he vomited from the pulpit, in the political harangues with which he polluted that place. I was honored with much of it. He is a man who can prove every thing if you will take his word for proof.” Such attacks on Jefferson were more commonly leveled by Congregationalists, “Rational Christians,” Unitarians, and “Deists” of New England who supported the Federalists—the opposing party of Jeffersonian Republicans.
Of course, as of the date of these pamphlets, Jefferson had only once expressed that he did not comprehend the Trinity, and did so totally private. He had never rejected Christianity or the Bible and had never said anything whatsoever about Deism, much less a profession of it. Jefferson’s report to James Madison on these false charges said that “…the republican papers of Massachusets & Connecticut continue to be filled with the old stories of deism, atheism, antifederalism &c.” The editors of The Papers of Thomas Jefferson give these comments regarding this letter to Madison: “John Beckley, characterizing the piece as a virulent portrayal of TJ ‘as an Atheist and Deist,’ countered it with a series of four articles…[and] DeWitt Clinton responded with essays…published in New York in 1800 as ‘A Vindication of Thomas Jefferson; Against the Charges Contained in a Pamphlet Entitled, ‘Serious Considerations,’ &c.’”
In short, there were political accusations against Jefferson being a Christian. Most of the people who knew him personally thought of him as a Christian. Meanwhile, later in life he did harbor privately some serious doubts about some key Christian doctrines. But he certainly was not a lifelong skeptic. During his strongest phase of life as a believer (by all outward appearances), Jefferson was most useful to his country—especially in writing the Declaration of Independence and the Virginia Statute for Religious Freedom.