"To compel a man to furnish contributions of money for the propagation of opinions which he disbelieves and abhors, is sinful and tyrannical." - Thomas Jefferson: Statute for Religious Freedom, 1779.
"[The clergy] believe that any portion of power confided to me [as President] will be exerted in opposition to their schemes. And they believe rightly: for I have sworn upon the altar of god, eternal hostility against every form of tyranny over the mind of man. But this is all they have to fear from me: and enough, too, in their opinion." - Thomas Jefferson to Benjamin Rush, 1800.
"The day will come when the mystical generation of Jesus, by the Supreme Being as his father, in the womb of a virgin, will be classed with the fable of the generation of Minerva in the brain of Jupiter." - Thomas Jefferson, Jefferson's Works, Vol. IV, p. 365, Randolph's ed.
The only way to square Jefferson is to understand that his actions on behalf of the federal government and those of the state of Virginia were different.