Jefferson claimed to be a Christian. Yet he seems to have redefined that term so as to make it mean what he wanted it to mean. Jefferson rejected most of the core beliefs of orthodox Christianity. He rejected the idea that Jesus was the Son of God. Rather, he viewed Jesus as a great moral teacher. He rejected biblical miracles, including the Resurrection. He asserted that the Apostle Paul had perverted the original teachings of Jesus. He even went so far as to create his own version of the Gospels, entitled The Life and Morals and Jesus of Nazareth, in which he removed all references to the miraculous (source: The Baker Encyclopedia of Christian Apologetics, pp. 378-380).
In fact, despite calling himself a Christian, Jefferson was essentially a deist. That is to say, he believed in a God who created the universe but did not intervene in human affairs. He believed that what God requires of us is that we act morally. He apparently believed in an afterlife and that there would be rewards and punishments in that afterlife for the deeds committed in this life. He was convinced that the apparent design of the universe was evidence for a Creator. He believed that Reason should guide our thinking.
In short, Jefferson was someone with whom both Christians and secularists in the 21st century would not be comfortable. He rejected Christian orthodoxy, yet he also implicitly rejected agnosticism and atheism. Nevertheless, in a way Jefferson's approach to religion is not that different from that of many modern-day Americans. Essentially, Jefferson adopted a sort of religion that he could be comfortable with, as do many today, opting for what sociologist Christian Smith has called moralistic therapeutic deism.
Nevertheless, I would argue that, on the whole, Jefferson's religious beliefs don't hold up under scrutiny. For one thing, as the great Christian apologist C. S. Lewis argued, a "great moral teacher" wouldn't go around claiming to be God when he knew it wasn't true, but Jesus did. Moreover, scholars now know that the epistles of Paul are probably the earliest documents in the New Testament. For example, the First Epistle to the Corinthians most likely dates to the mid-50s AD, within twenty years or so of the Crucifixion. Given this relatively short interval of time, it seems unlikely that Paul would have been able to distort the teachings of Jesus without being called out for it by those who had heard those teachings.
Even so, I think Jefferson should still be given credit for affirming in such eloquent language the inherent equality of all human beings--an idea which, whether he would have acknowledged it or not--has its origin in the Christian belief that all are created in the image of God.
Image: Rembrandt Peale's portrait of Thomas Jefferson from Wikimedia Commons