Jefferson is known as "The Sphinx" for a good reason. He knew how to play politics. The Federalists knew he was an atheist and accused him as such:
Accusations of being an infidel
During the 1800 presidential campaign, the New England Palladium wrote, "Should the infidel Jefferson be elected to the Presidency, the seal of death is that moment set on our holy religion, our churches will be prostrated, and some infamous 'prostitute', under the title of goddess of reason, will preside in the sanctuaries now devoted to the worship of the most High."[30] Federalists attacked Jefferson as a "howling atheist" and infidel, claiming that his attraction to the religious and political extremism of the French Revolution disqualified him from public office.[31][32] At that time, calling a person an infidel could mean a number of things, including that they did not believe in God. It was an accusation commonly levelled at Deists, although they believe in a deity. It was also directed at those thought to be harming the Christian faith in which they were raised.
While opposed to the institutions of organized religion, Jefferson consistently expressed his belief in God. For example, he invoked the notion of divine justice in 1782 in his opposition to slavery,[33] and invoked divine Providence in his second inaugural address.[34]
Jefferson did not shrink from questioning the existence of God. In a 1787 letter to his nephew and ward, Peter Carr, who was at school, Jefferson offered the following advice:
“ 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 of blindfolded fear. ... Do not be frightened from this inquiry by any fear of its consequences. If it end in a belief that there is no God, you will find incitements to virtue in the comfort and pleasantness you feel in its exercise and in the love of others which it will procure for you. -- (Jefferson's Works, Vol. ii., p. 217)[35] ”
Following the 1800 campaign, Jefferson became more reluctant to have his religious opinions discussed in public. He often added requests at the end of personal letters discussing religion that his correspondents be discreet regarding its contents.[6]