In July 1873, author James Parton wrote a lengthy essay in Atlantic Magazine about the 1800 campaign. Parton shows how religion was an important issue in the ugly 1800 election, pointing out that some of the ministers didn’t shy from speaking out on politics:
“The orthodox clergy were not averse, then, it appears, to “politics in the pulpit.” Our historical collections yield many proofs of it in the form of pamphlets and sermons of the year 1800. It cheers the mind of the inquirer, in his dusty rummaging, to measure the stride the public mind has taken in less than three quarters of a century.”
Some 75 years later, seems to sneer Mr. Parton, we know better than to see politics addressed in the pulpit.
“Hold!” cries one vigorous lay sermonizer (Claims of Thomas Jefferson to the Presidency examined at the Bar of Christianity),—”hold! The blameless deportment of this man has been the theme of encomium [i.e., glowing praise]. He is chaste, temperate, hospitable, affectionate, and frank.” But, he is no Christian! He does not believe in the deluge. He does not go to church. “Shall Thomas Jefferson,” asks this writer, “who denies the truth of Christianity, and avows the pernicious folly of all religion, be your governor?”
Jefferson may have the character of a Christian, declares a pulpiteer, but he denies the truth of the religion. Shall he be elected to rule over us? Parton cites other examples of the minister’s attacks against Jefferson in the election of 1800:
“One writer proves his case thus: 1. The French Revolution was a conspiracy to overthrow the Christian religion; 2. Thomas Jefferson avowed a cordial sympathy with the French Revolution; 3. Therefore, Thomas Jefferson aims at the destruction of the Christian religion. To this reasoning facts were added. Mr. Jefferson, fearing to trust the post-office, had written a letter in Latin to an infidel author, approving his work and urging him to print it. Then look at his friends! Are they not ‘deists, atheists, and infidels’? Did not General Dearborn one of his active supporters, while traveling to Washington in a public stage, say, that ‘so long as our temples stood, we could not hope for good order or good government’? The same Dearborn, passing a church in Connecticut, pointed at it, and scornfully exclaimed, ‘Look at that painted nuisance!’ But the most popular and often-repeated anecdote of this nature, which the contest elicited, was the following: ‘When the late Rev. Dr. John B. Smith resided in Virginia, the famous Mazzei happened one night to be his guest. Dr. Smith having, as usual, assembled his family for their evening devotions, the circumstance in which the Italian made no secret of his infidel principles. In the course of conversation, he remarked to Dr. Smith, “Why, your great philosopher and statesman, Mr. Jefferson, is rather further gone in infidelity that I am”; and related, in confirmation, the following anecdote. That as he was once riding with Mr. Jefferson, he expressed his “surprise that the people of this country take no better care of their public buildings.” “What buildings?” exclaimed Mr. Jefferson. “Is not that a church?” replied he, pointing to a decayed edifice. “Yes,” answered Mr. Jefferson. “I am astonished,” said the other, “that they permit it to be in so ruinous a condition.” “It is good enough,” rejoined Mr. Jefferson, “for him that was born in a manger!” Such a contemptuous fling at the blessed Jesus could issue from the lips of no other than a deadly foe to his name and his cause.’”
In reality, Mazzei was, with Jefferson, a fellow-member of the Calvinistical Reformed Church in Charlottesville, and extremely unlikely to have told this story at all but certainly not as disparaging of Jefferson as Smith seemed to have taken it. Jefferson responded to it elsewhere as a complete fabrication. The overall point? The narrative of Jefferson the lifelong skeptic is not an accurate picture.
 James Parton, “The Presidential Election of 1800,” Atlantic Magazine, July 1873. http://www.theatlantic.com/magazine/archive/1873/07/the-presidential-election-of-1800/307019/?single_page=true.