In July 1873, author James Parton wrote a lengthy essay in Atlantic Magazine about the 1800 campaign. It is interesting for it provides an analysis by a writer somewhat closer to those events than scholars today, and it attempted to correct some of the inaccurate portrayal of Jefferson in the previous half-century. Parton was a popular American nineteenth century biographer. He notes that religion’s role in the 1800 election apparently was unique (at least at the time he was writing this article in 1873):
“Religion, for the first and last time, was an important element in the political strife of 1800. There was not a pin to choose between the heterodoxy of the two candidates [Neither Adams nor Jefferson were orthodox.]; and, indeed, Mr. Adams was sometimes, in his familiar letters, more pronounced in his dissent from established beliefs than Jefferson.”
Parton looks back, condescendingly, upon previous ages of faith. He sees John Adams having less patience with those, for example, who wrote the Nicene Creed in 325 a.d. than did Thomas Jefferson. Parton continues:
“Mr. Adams, however, was by far the more impatient of the two with popular creeds, as he shows in many a comic outburst of robust and boisterous contempt. …As for the doctrine of the Trinity, he greatly surpassed Jefferson in his aversion to it. He scolded Jefferson for bringing over European professors, because they were ‘all infected with Episcopal and Presbyterian creeds,’ and ‘all believed that great Principle [Jesus], which has produced this boundless universe, Newton’s universe and Herschel’s universe, came down to this little ball, to be spit upon by Jews.’ Mr. Adams’s opinion was, that ‘until this awful blasphemy was got rid of, there will never be any liberal science in this world.’”
Here is a strong anti-faith sentiment from John Adams, dismissing the notion that Jesus—who subjected Himself to rejection by the Jews—was the One who created the universe. Assuming Parton’s reading of Adams is correct, it should be noted that the early scientists, including Isaac Newton, had a largely Christian worldview. In the words of Johannes Kepler, the great astronomer, they were “thinking God’s thoughts after Him.” But Adams seems to be saying that science (knowledge) will not succeed until orthodox religion is gone. Assuming this is correct, Adams thus creates a false either/or. Parton wonders how Adams escaped censure; he then adds more details about the Rev. Mason and Rev. Linn, cited above:
And yet he [Adams] escaped anathema. Mr. Jefferson, on the contrary, was denounced by the pious and moral Hamilton as “an atheist.” The great preacher of that day in New York was Dr. John Mason, an ardent politician, as patriotic and well-intentioned a gentleman as then lived. He evolved from Jefferson’s Notes on Virginia the appalling truth, that the Republican candidate for the Presidency did not believe in the universal deluge! (Jefferson’s party were often called Republicans or Democratic Republicans. The opposing party, that of John Adams, was the Federalist Party.)
That is, Dr. Mason is accusing Jefferson of not believing in Noah’s flood. Parton continues about Mason:
“He sounded the alarm. A few weeks before the election, he published a pamphlet entitled The Voice of Warning to Christians on the ensuing Election; in which he reviewed the Notes, and inferred, from passages quoted, that the author was ‘a profane philosopher and an infidel.’ ‘Christians!’ he exclaimed, ‘it is thus that a man, whom you are expected to elevate to the chief magistracy, insults yourselves and your Bible!’ An interesting character was this Dr. Mason, if we may believe the anecdotes still told of him by old inhabitants of New York. What a scene must that have been when he paused, in the midst of one of his rousing Fast Day sermons, and, raising his eyes and hands to Heaven, burst into impassioned supplication: ‘Send us, if Thou wilt, murrain upon our cattle, a famine upon our land, cleanness of teeth in our borders; send us pestilence to waste our cities; send us, if it please Thee, the sword to bath itself in the blood of our sons; but spare us, Lord God Most Merciful, spare us that curse,—most dreadful of all curses,—an alliance with Napoleon Bonaparte!’”
Jefferson, of course, had served in France from 1782-1789 as our ambassador. He clearly had some sympathies with the French and was thus viewed with suspicion. Jefferson was long gone from there before Napoleon arose. Parton continues his description of the New York minister, Dr. John Mason:
“An eye-witness reports that, as the preacher uttered these words, with all the energy of frantic apprehension, the blood gushed from his nostrils. He put his handkerchief to his face without knowing what he did, and, instantly resuming his gesture, held the bloody handkerchief aloft, as if it were the symbol of the horrors he foretold. To such a point, in those simple old days, could campaign falsehood madden able and good men!”
With emotional fervor, falsehood—even in the pulpit—could fool otherwise good citizens.
Again, none of this antipathy against Jefferson was found in the pulpits south of New York state.
What is the take home message of all this? Part of the reason that we have the Jefferson-as-skeptic message was fallout from the 1800 election, where he was accused of being such. Such accusations were to be found not among those who knew him, but among those in the northern (they called them “eastern” states). This even included Unitarians from New England. Some of the mud slung in the 1800 election at Jefferson, alas, has stuck for a couple of centuries now. He would say unfairly….as he opened up his Bible for personal edification.
 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.
 Parton, “The Presidential Election of 1800.”
 For example, Sir Isaac Newton said, “I have a foundational belief in the Bible as the Word of God, written by men who were inspired. I study the Bible daily.” D. James Kennedy and Jerry Newcombe, What If Jesus Had Never Been Born? (Nashville: Thomas Nelson, Publishers, 1994 /2001), 100.
 Kennedy and Newcombe, 99.
 Parton, “The Presidential Election of 1800.”