Doubting Thomas deals with the faith of Jefferson and his views of what should and what shouldn’t be allowed of religion in the public arena. We show that Jefferson went through different stages of belief to questioning to private doubts to private skepticism, etc. We document that he was not a lifelong skeptic.
I think it’s safe to say that when the founding fathers began the process of Independence through the time of establishing the Constitution, they looked to God more frequently than they did later, when things settled down. Jefferson was more God-reliant earlier in his life than he was later. In fact, one can find pro-faith statements from some of the founding fathers during the time of Independence that are contrasted with anti-faith statements (or anti-Trinitarian comments) that come later—usually after they retired from public life.
For example, Thomas Paine mentioned God positively in his 1776 book, Common Sense. By the early 1790s, he was writing vicious attacks against the Christian faith, e.g., The Age of Reason. When he was of value to the American cause, he was pro-Christian. John Adams wrote some important statements, such as this one: “Our Constitution was made only for a moral and religious people. It is wholly inadequate to the government of any other.” Later, he and Abigail embraced Unitarianism and jettisoned historic Christianity. The same seems to be true of Jefferson.
Here’s the question for historians to ponder. Do we then take the anti-faith statements made late in life and use these to nullify the pro-faith statements early in life? Is that fair? Is that accurate? In all these and other cases, the pro-faith statements were made while the founding father in question was useful to the cause of American freedom and the creation of our government. The anti-faith statements were made later, after retirement. It is conceivable that some of them could have been, possibly, the results of old age. This is pure speculation. But here’s the question: Why should Jefferson’s questionings in the 1820s (long after his service to our country) be used to cast doubt on his earlier pro-faith statements?
Robert Cord makes a similar point when rebutting the later thoughts of James Madison on church and state matters. Dr. Cord was the University Distinguished Professor of Political Science at Northeastern University and author of Separation of Church and State: Historical Fact and Current Fiction. When James Madison was old and long retired, he wrote a “Detached Memoranda,” where he felt that he erred when he was younger in voting for chaplains as a legislator and in declaring national days of prayer and thanksgiving as president.
ACLU attorney and professor Leo Pfeffer said essentially: Ignore the earlier Madison; listen only to the later Madison. Here’s what Cord writes about that:
Whereas Pfeffer rests his argument about chaplains in Congress and Thanksgiving Proclamations on one document written in Madison’s declining years. I think that Madison should be judged on his behavior, statements and actions while he was a public servant in the House and in the Presidency making policy and accountable for it. An analogous contemporary illustration should make my point. If former President Nixon, reflecting on his tenure as President, in his final years were to publish a book in which he unequivocally wrote that: “Taping conversations, without all parties being aware of the recording, is morally wrong and clearly a fragrant violation of the constitutional right of privacy,” then in my judgment, it would be absurd—for any future biographer or analyst evaluating Mr. Nixon as President—to write that: “Richard Nixon believed that surreptitious tapings of conversations in the Oval Office were immoral and unconstitutional.” Indeed, the “Detached Memoranda” is appropriately named, for it reflects ideas certainly “detached” from views Madison expounded in Congress and the White House.
In the same way, when Jefferson was useful to the American cause of liberty and religious freedom, it was during a period of his strongest Christian belief. The founders, including Jefferson, appeared to be more religious when they needed God the most.
 John Adams, October 11, 1798, in a letter to the officers of the First Brigade of the Third Division of the Militia of Massachusetts. Charles Francis Adams (son of John Quincy Adams and grandson of John Adams), ed., The Works of John Adams – Second President of the United States: with a Life of the Author, Notes, and Illustration (Boston: Little, Brown, & Co., 1854), Vol. IX, pp. 228-229.
 Robert L. Cord, Separation of Church and State: Historical Fact and Current Fiction (Grand Rapids, MI: Baker Book House, 1988).
 Robert L. Cord, Separation of Church and State: Historical Fact and Current Fiction (Grand Rapids, MI: Baker Book House, 1988), 36.