He wrote of disbelieving in the divinity of Christ--yet, Jefferson remained on the vestry of his local Church--and never made a break with membership in the Church.
The infamous "Jefferson Bible" is also usually misunderstood. This is his version of the gospels where he cut out all the miracles of Christ.
He did not write that bible for himself....or pretend he thought it was what the "real" bible should be, rather he attempted to write a book of Jesus' morality to share with the American Indians...so they wouldn't have to deal with question (and skepticism toward) Jesus miracles. Of course it was futile and a failure--Jesus message, morality, and miracles simply cannot be rationally separated--but Jefferson surely was an enlightenment era skeptic to try.
I think it's fair to say while the winds of Deism blew strong amidst the founders (part of the cultural climate of the day), very few (perhaps Franklin alone) were actually full blown, consistent deists. Paine took deism to it's logical end...an absent God is pretty much the same as no God.
I would have a hard time voting for an atheist, even if I agreed with his policies....mainly because I don't know how he would have a basis of ethics. As Dostoevsky's Ivan indicated (though never actually said...), without God all things are permissible. The most powerful atheists who ever ruled have shown how this worked out: Hitler, Stalin, Pol Pot, Mao..... with hundreds of millions of victims' blood on their hands.
He contemporaneously records his intent of the “Jefferson Bible” as for his own use, saying...
“In the moment of my late departure from Monticello, I received from Dr. Priestley his little treatise of “Socrates and Jesus Compared.” This being a section of the general view I had taken of the field, it became a subject of reflection while on the road and unoccupied otherwise. The result was, to arrange in my mind a syllabus or outline of such an estimate of the comparative merits of Christianity as I wished to see executed by someone of more leisure and information for the task than myself. This I now send you as the only discharge of my promise I can probably ever execute. And in confiding it to you, I know it will not be exposed to the malignant perversions of those who make every word from me a text for new misrepresentations and calumnies. I am moreover averse to the communication of my religious tenets to the public”
He also describes his purpose in “I think you cannot avoid giving, as preliminary to the comparison, a digest of his moral doctrines, extracted in his own words from the Evangelists, and leaving out everything relative to his personal history and character. It would be short and precious. With a view to do this for my own satisfaction, I had sent to Philadelphia to get two testaments (Greek) of the same edition, and two English, ?with a design to cut out the morsels of morality, and paste them on the leaves of a book”