The returning good sense of our country threatens abortion to hopes, & they believe that any portion of power confided to me, 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: & enough too in their opinion, & this is the cause of their printing lying pamphlets against me, forging conversations for me 
Difference of opinion is advantageous in religion. The several sects perform the office of a Censor morum over each other. Is uniformity attainable? Millions of innocent men, women and children, since the introduction of Christianity, have been burnt, tortured, fined, imprisoned: yet we have not advanced one inch towards uniformity. What has been the effect of coercion? To make one half the world fools, and the other half hypocrites. To support roguery and error all over the earth. 
The rights of conscience we never submitted, we could not submit. We are answerable for them to our God. The legitimate powers of government extend to such acts only as are injurious to others. But it does me no injury for my neighbour to say there are twenty gods, or no god. It neither picks my pocket nor breaks my leg. … Reason and free enquiry are the only effectual agents against error. 
Fix reason firmly in her seat, and call to her tribunal every fact, every opinion. Question with boldness even the existence of a god; because, if there be one, he must more approve the homage of reason, than that of blindfolded fear. 
And 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. But we may hope that the dawn of reason and freedom of thought in these United States will do away all this artificial scaffolding, and restore to us the primitive and genuine doctrines of this the most venerated reformer of human errors. 
In fact is so incomprehensible to the human mind that no candid man can say he has any idea of it, and how can he believe what presents no idea. He who thinks he does only decieves himself. He proves also that man, once surrendering his reason, has no remaining guard against absurdities the most monstrous, and like a ship without rudder is the sport of every wind. With such persons gullability which they call faith takes the helm from the hand of reason and the mind becomes a wreck. [sic] 
Thomas Jefferson, third President of the United States:
 letter to Dr. Benjamin Rush, 1800-10-23 Note that he specifically indicates that he will take no action against the church leaders that smeared him; all they have to fear is his hostility and ill will.
 Notes on the State of Virginia Jefferson here stated explicitly that he saw atheism as an inalienable right, and outside the province of the State.
 letter to Peter Carr, 1787-08-10 In other words, agnosticism is preferable to blind faith.
 letter to John Adams, 1823-04-11 Note that he held Jesus’s principles in high regard, but rejected the christian mythology just the same. It was his hope that the free and secular nature of the American society would bring about the demise of these beliefs.
 letter to James Smith, 1822-12-08