Mostly, Jefferson was against the Calvinistic approach to Christianity. It should be noted that he appreciated Christ's teaching but did not accept the miraculous aspects of Christ's acts. This is the basis of his Syllabus of an Estimate of the Merit of the Doctrines of Jesus (commonly known as the "Jefferson Bible").
My aim in that was, to justify the character of Jesus against the fictions of his pseudo-followers, which have exposed him to the inference of being an impostor. For if we could believe that he really countenanced the follies, the falsehoods and the charlatanisms which his biographers father on him, and admit the misconstructions, interpolations and theorizations of the fathers of the early, and fanatics of the latter ages, the conclusion would be irresistible by every sound mind, that he was an impostor. I give no credit to their falsifications of his actions and doctrines, and to rescue his character, the postulate in my letter asked only what is granted in reading every other historian.... That Jesus did not mean to impose himself on mankind as the son of God, physically speaking, I have been convinced by the writings of men more learned than myself in that lore.
-- Thomas Jefferson, letter to William Short, August 4, 1820, explaining his reason for compiling the Syllabus of an Estimate of the Merit of the Doctrines of Jesus and referring to Jesus's biographers, the Gospel writers.
We must reduce our volume to the simple evangelists, select even from the very words of Jesus, paring off the amphiboligisms into which they have been led by forgetting often or not understanding what had fallen from him, by giving their own misconceptions as his dicta, and expressing unintelligibly for others what they had not understood themselves. There will be found remaining the most sublime and benevolent code of morals which has ever been offered to man. I have performed this operation for my own use, by cutting verse by verse out of the printed book, and arranging the matter which is evidently his, and which is as easily distinguishable as diamonds in a dunghill.
-- Thomas Jefferson, letter to John Adams, October 13, 1813, clarifying his desire to strip away the myth introduced by the Gospel writers, as his motivation for constructing his Syllabus of an Estimate of the Merit of the Doctrines of Jesus