Doubting Thomas deals with the issue of Jefferson’s faith and actually provides some new material in it never before published, ever. The book shows that he was not a lifelong skeptic. Near the end of his life, he had some private unorthodox views. I like to say: Jefferson was a great statesman, but a lousy theologian.
Jefferson is not always easy to pin down, as to his religious views. Jefferson was positively influenced by the Bible, but he had a rationalistic approach to it. I doubt Jefferson was trusting in Christ’s finished work on the cross. But that doesn’t mean he didn’t make significant contributions to the cause of freedom, even the Christian cause. We must bear true witness to the real Thomas Jefferson. Although Jefferson did not embrace orthodox, historic Christianity, he was still positively influenced by it.
No one should say Jefferson was an evangelical. But nor should anyone say he was an atheist. One of the key questions about Jefferson is what did he think about religious liberty?
Jefferson stands for a very important principle. He is in the tradition of Rev. Roger Williams, founder of Rhode Island, and William Penn, founder of Pennsylvania—standing for freedom of conscience.
During his lifetime, some of the strongest criticisms against Jefferson on religion were leveled at him because of his belief in disestablishment. He helped disestablish the official state-church in Virginia, i.e., the Anglican Church “by law established.” In his own day, many critics of Jefferson confused his disestablishmentarianism with anti-church sentiments. They were wrong, just as are modern critics of Jefferson who see him as a complete infidel. (Nor are we saying he was orthodox, certainly not by the end of his life.)
Daniel Dreisbach, political science professor at American University and author of Thomas Jefferson and the Wall of Separation of Church and State says this about Thomas Jefferson:
Jefferson described himself as “a real Christian,” although he was certainly aware that his beliefs were unconventional. “I am of a sect by myself,” he said. He believed that human reason was the arbiter of religious truth and rejected key tenets of orthodox Christianity, including the Bible’s divine origins, the deity of Christ, original sin, and the miraculous accounts in Scripture. Jefferson’s faith provided an early test of religion’s place in national politics. His heterodox beliefs raised doubts about his fitness for high office.
We are familiar with the phrase from our military, “An Army of One.” In one sense, Jefferson viewed himself as a “church of one.” And yet, he was actually a lifelong churchman. He went to church whenever he could. Not just liberal, way out there churches. He did like to attend the Unitarian church in Philadelphia. We don’t know about any church-going in France, where he served as our ambassador from 1782-1789. But for the bulk of his life, early and late (and while he was president), he attended church virtually on a weekly basis. He was a tithing member of the Anglican church.
Thomas Jefferson based his views of religious freedom on the notion that Jesus is the source of our freedoms. Since Jesus didn’t impose Himself on anyone, nor should the government force people to believe what they believe. One history professor at a Christian College once asked co-author Jerry Newcombe on his radio show, “Who cares whether Jefferson was a true Christian or not?” His response, “Well, it matters for Jefferson himself, in terms of his own salvation.” But the point of the professor is well-taken. In one sense, only God knows who is (or who was) truly His.
 Daniel Dreisbach, “The rancorous presidential election of 1800 brought religion to the forefront of public debate and had lasting repercussions for the relationship between church and state” Christian History & Biography Magazine, Issue #99 (Wall of Separation), 2008. http://www.christianhistorymagazine.org/index.php/past-pages/99separation/