Those who knew Jefferson personally thought that he was a Christian. Most of the critics of his faith or the lack thereof arose after his death. But there were contemporary accusations against Jefferson for supposedly not being a Christian. Many of these accusations, as mentioned in previous blogs, arose during the 1800 election—a terrible time of mud-slinging.
James Parton wrote an article in 1873 on the faith of Jefferson and the election of 1800. Based on what he wrote, John Adams appears to be more anti-orthodox in his opinions than was Jefferson.
Parton said he did not understand how other contemporaries of Jefferson (such as James Madison) came out unscathed, but not the third president:
“It is not clear, upon the first view of this subject, why Jefferson should have been singled out for reprobation on account of a heterodoxy in which so many of the great among his compeers shared. He attributed it himself to the conspicuous part he had taken in the separation of Church and State in Virginia; a policy which the clergy opposed with vehemence, in each State, until, in 1834, the divorce was complete and universal by the act of Massachusetts. Readers of Dr. Lyman Beecher’s Autobiography remember how earnestly that genial hunter before the Lord fought the severance in Connecticut.”
Parton is showing here what Jefferson himself believed—that much of the opposition of the clergy against Jefferson was because of his views on disestablishmentarianism. Jefferson didn’t believe in an established church, not even on the state level. That does not mean that he opposed the church per se. He continues:
“Some of the clergy, Jefferson thought, cherished hopes of undoing the work done in Virginia and other States through Madison, Wythe, and himself. But, said he, ‘the returning good sense of our country threatens abortion to their hopes, and 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.’”
On this point, Jefferson and the ministers who wanted established state churches could agree: that Jefferson was opposed to established government churches (even at the state level).
He avoided, on principle, that line of conduct, so familiar to public men of the fourth, fifth, and sixth rank, which Mark Twain has recently called “currying favor with the religious element.”
While he was most careful not to utter a word, in the hearing of young or unformed persons, even in his own family, calculated to disturb their faith, he was equally strenuous in maintaining his right to liberty both of thought and utterance. Thus, at a time when the word “Unitarian” was only less opprobrious than infidel, and he was a candidate for the Presidency, he went to a church of that denomination, at Philadelphia, in which, as he says, “Dr. Priestley officiated to numerous audiences.” “I never will,” he once wrote, “by any word or act, bow to the shrine of intolerance or admit a right of inquiry into the religious opinions of others. On the contrary, we are bound, you, I, and every one, to make common right of freedom of conscience. We ought, with one heart and one hand, to hew down the daring and dangerous efforts of those who would seduce the public opinion to substitute itself into that tyranny over religious faith which the laws have so justly abdicated. For this reason, were my opinions up to the standard of those who arrogate the right of questioning them, I would not countenance that arrogance by descending to an explanation.” It strengthened Jefferson’s faith in republican institutions, that his countrymen rose superior to religious prejudices in 1800, and gave their votes very nearly as they would if the religious question had not been raised.
Jefferson boldly speaks out here on behalf of freedom of conscience. It should not be stifled. Today, we might add, we find the tyranny of political correctness—state-sanctioned atheism—is squelching freedom of conscience for those who disagree.
 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.