When it comes to religion and understanding Thomas Jefferson, it is a complicated picture. But our book by Mark Beliles and me, Doubting Thomas, makes two points that are well-documented. 1) Jefferson was not a lifelong skeptic. Earlier in life, when he was most important as a founding father, by all outward appearances he was a Christian and attending Trinitarians services. Later he did come to privately question core Christian doctrines. 2) Jefferson did not believe in the separation of church and state, in the way it is understood today, essentially, as the separation of God and state.
The life of Jefferson, including when he was president, shows that he had many interactions with all sorts of Christians. For example, a group of Baptist churches wrote to Jefferson with appreciation at this time on May 20, 1806 from “…the North Carolina Chowan Association, held at Salem, on Newbiggin Creek, in the District of Edenton, & State of North Carolina…”
Jefferson replied on June 24th “…with gratitude to the being under whose providence these blessings are held. we owe to him especial thanks for the right we enjoy to worship him, everyone in his own way…” Over a year later a sixth group of Baptists wrote to the President to commend him and wish for his party to continue in power since he was planning to not seek reelection. They were “…of the Appomattox Association within the County of Prince Edward & the Counties adjacent.” Jefferson replied to them with similar words on December 21, 1807.
And a year after that Rev. William Tristoe and Rev. Thomas Buck wrote to Jefferson on behalf of a seventh group of Baptists, the Ketockton Baptist Association meeting in Loudoun County, Virginia. They reminded him of presenting their petition for religious freedom a quarter of a century earlier, saying “…We have not forgotten that, into your hand, our petition on this interesting subject was put.”
Jefferson’s Reply was October 18, 1808: “…although your favor selected me as the organ of your petition to abolish the religious denomination of a privileged church, yet I was but one of the many who befriended its object, and am entitled but in common with them to a portion of that approbation which follows the fulfillment of a duty.…a recollection of our former vassalage in religion and civil government will unite the zeal of every heart, and the energy of every hand, to preserve that independence in both, …and I return your kind prayers by supplications to the same Almighty Being for your future welfare, and that of our beloved country.”
Either Jefferson was a big hypocrite—constantly referring to God and prayer—or the modern caricature of him as a lifelong skeptic was wrong. The preponderance of evidence shows that he was not a lifelong unbeliever.