Although Jefferson clearly condemned church-state clergy in Europe and in the northeastern parts of the United States, he had a completely different view of clergy in Virginia for most of his last several decades. In late 1813 Jefferson wrote John Adams saying that here “. . . The law for religious freedom . . . [in Virginia has] put down the aristocracy of the clergy and restored to the citizen the freedom of the mind.”
But a misunderstanding over hiring of professors at the University of Virginia brought forth criticism from him of clergy in that state for the first time.
Initially, an evangelical Presbyterian clergyman, Samuel Knox, was offered the first job to be a professor at the school, but the invitation did not receive his attention in time. But shortly after Knox’s invitation was sent, a second professor was hired, a Unitarian, Thomas Cooper, to teach chemistry. Cooper had a reputation as being dogmatic in his opposition to the doctrine of the Trinity.
Presbyterians who had been vocal in favor of the non-sectarian nature of the school did not know of the first invitation to Rev. Knox, so they now felt betrayed by this job offer. They raised such a fuss that the school rescinded the offer to Cooper. All of this left Thomas Jefferson angered, for the first time we know of, at the Presbyterians. You can read more details about this conflict in chapter 11 on the University of Virginia.
On March 13, 1820, Jefferson wrote to Cooper: “. . . the Presbyterian clergy alone (not their followers) remain bitterly federal and malcontent with their government, they are violent, ambitious of power, and intolerant in politics as in religion and want nothing but license from the laws to kindle again the fires of their leader John Knox, and to give us a 2d blast from his trumpet. Having a little more monkish learning than the clergy of the other sects, they are jealous of the general diffusion of science [i.e., knowledge], and therefore hostile to our Seminary lest it should qualify their antagonists of the other sects to meet them in equal combat. . . .”
Jefferson wrote to Catholic friend Rev. José Correia da Serra on April 11, 1820, to explain the situation: “[in] . . . our University; . . . There exists indeed an opposition to it by the friends of William and Mary, which is not strong. The most restive is that of the priests of the different religious sects, who dread the advance of science as witches do the approach of day-light; and scowl on it the fatal harbinger announcing the subversion of the duperies on which they live. In this the Presbyterian clergy take the lead. The tocsin is sounded in all their pulpits. . . .”
Jefferson continued on this theme in a letter to confidant and former assistant, William Short, on April 13, 1820:
“The history of our University you know so far. . . . The serious are the priests of the different religious sects, to whose spells on the human mind its improvement is ominous. Their pulpits are now resounding with denunciations against the appointment of Doctor Cooper, whom they charge as a monotheist in opposition to their tritheism. Hostile as these sects are, in every other point, to one another, they unite in maintaining their mystical theogony against those who believe there is one God only. The Presbyterian clergy are loudest; the most intolerant of all sects, the most tyrannical and ambitious ; ready at the word of the lawgiver, if such a word could be now obtained, to put the torch to the pile, and to rekindle in this virgin hemisphere, the flames in which their oracle Calvin consumed the poor Servetus, because he could not find in his Euclid the proposition which has demonstrated that three are one and one is three, nor subscribe to that of Calvin, that magistrates have a right to exterminate all heretics to Calvinistic Creed. They pant to re-establish, by law, that holy inquisition, which they can now only infuse into public opinion.”
The references to Euclid mean that Jefferson’s understanding of the Trinity did not square with the mathematical findings of the ancient Greek thinker. Michael Servetus was a Unitarian who preached in Calvin’s Geneva and was put to death for it in what is one of the blackest events of the Reformation.
To Unitarian Thomas Cooper Jefferson writes November 2, 1822, saying: “. . . In our Richmond there is much fanaticism, but chiefly among the women . . . attended by their priests. . . .”
Although clergy criticized the university’s hiring of a Unitarian not once was Jefferson’s faith itself attacked or questioned by these Virginian ministers. But Jefferson released some of his harshest criticisms of them, and of Presbyterians in particular for the very first time in his entire life. It was an unfortunate misunderstanding that was brief and not lasting.
It is an error to interpret this conflict to arise from a desire in Jefferson to have all clergy excluded from in his state university. Besides offering a professorship to Rev. Knox, Jefferson also offered a professorship to Anglican Rev. Samuel Parr in 1824. Parr declined due to age and health but clearly there was no general anti-clerical bias held by Jefferson.
 Letter to John Adams, October 28, 1813. www.founders.archives.gov.
 Letter to Thomas Cooper, March 13, 1820.
 Letter to Rev. Correa da Serra, April 11, 1820.
 Letter to William Short, April 13, 1820. Dickinson Adams, 391.
 Letter to Thomas Cooper, November 2, 1822. Ford, The Works, vol. 12.
[File photo by Jerry Newcombe. It is St. Matthews church in Nassau, Bahamas]