Jefferson was not as anti-clerical as he is often thought to be today. He certainly criticized state-churches and abuse of power by clergy. Jesus Himself was delivered over to be crucified by a type of state-clergy.
The criticism of European clergy in politics is consistent but it was different in Virginia. At the very end of 1784 Jefferson sends a letter from France to lawyer James Madison who was pushing for religious freedom in the Virginia legislature. Madison informed Jefferson that the Episcopal clergy were pushing for legal incorporation status for their church. Jefferson responded that “. . . the Episcopalians have again shewn their teeth and fangs. . . .” This was the first critical statement that Jefferson ever expressed about Episcopalians (and perhaps clergy] in America. All other comments before then were about priests in European history or early America (as he did in his Notes on Virginia).
Jefferson cited in various letters home of his desire to see religious freedom succeed in Virginia and in a letter to Marquis de Chastellux on September 2, 1785 he defended (even though he was not responsible for) the Virginia Constitution’s prohibition of clergy in public office: “The clergy are excluded, because, if admitted into the legislature at all, the probability is that they would form it’s majority. For they are dispersed through every county in the state, they have influence with the people, and great opportunities of persuading them to elect them into the legislature. This body, tho shattered, is still formidable; . . . (and) merit a proscription from meddling with government.”
But Jefferson reversed this opinion a decade-and-a-half later. On August 14, 1800, Jefferson replied to a letter from Baptist Rev. Jeremiah Moore, saying: “. . . after 17 years more of experience and reflection, I do not approve [a clause in the Virginia constitution]. It is the incapacitation of a clergyman from being elected. The clergy, by getting themselves established by law, & ingrafted into the machine of government, have been a very formidable engine against the civil and religious rights of man. They are still so in many countries & even in some of these United States. . . .”
That place in the United States where clergy still posed problems was in the northeastern states where the Federalist Party was strong. His first criticism of northern clergymen took place in a letter to James Madison dated March 2, 1798 when he said that the New England states “are so priest-ridden, that nothing is to be expected from them, but the most bigoted passive obedience.”And Jefferson wrote his friend Bishop James Madison of Virginia on January 31, 1800, saying: “. . . [Jedidiah] Morse . . . & his ecclesiastical and monarchical associates [in Massachusetts] have been making such a hue and cry.” Rev. Morse led the Congregational alliance with the Federalist Party in New England in opposition to Jefferson’s party.
Thus, it is a false notion of Jefferson as some sort of anti-minister politician.