Jefferson had harsh words for any clergy who abused political power through his office. But that does not mean he condemned all clergy who he knew that were involved in politics.
The 1777 church Subscription document Jefferson drafted reported that during the Revolutionary War Rev. Charles Clay was known for his prayers that “. . . ever addressed the God of battles for victory to our arms.”
In 1779 Jefferson praised Rev. Clay’s religious-based patriotism in a testimonial letter which said of him: “[H]is deportment has been exemplary. . . ; In the earliest stage of the present contest with Great Britain, while the clergy of the established church in general took the adverse side, or kept aloof from the cause of their country, he took a decided and active part with his countrymen, and has continued to prove his Whiggism unequivocal, and his attachment to the American cause to be sincere and zealous.”
While in France Jefferson came to know “The Archbishop of Toulouse [Etienne Charles Lomenie de Brienne]” and he explained in a letter to John Adams on August 30, 1787, that the archbishop was “a virtuous . . . character . . . in reforming the cruel abuses of the government and preparing a new constitution. . . .” He wrote James Madison on June 18, 1789, saying that within Catholicism: “the mass of the Clergy . . . are . . . favorably known to the people . . . and united with them.” And to John Jay a few days later: “. . . the Chamber of the Clergy . . . found the doors shut and guarded . . . ; The next day they met in a church and were joined by a majority of the Clergy . . . They protested against what the King had done.”
Jefferson supported clergy in America getting involved in government—although there was a time when he felt that the Anglican clergy had an unfair advantage in Virginia politics, so he agreed (initially) with a measure to curb their political involvement. Meanwhile, he writes Rev. Clay on January 27, 1790: “I understand you are a candidate for . . . Congress; . . . I am sure I shall be contented with such a representative as you will make; . . . Wishing you every prosperity in this . . . undertaking; . . . your friend & servant.”
On August 14, 1800, Jefferson replied to a letter from Baptist Rev. Jeremiah Moore, saying:
“You may remember perhaps that in the year 1783 . . . [a clause was added to the Virginia] constitution, an abridgement of the right of [clergy] being elected, which after 17 years more of experience and reflection, I do not approve. 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; . . . It now appears that our means were effectual. The clergy here seem to have relinquished all pretension to privilege and to stand on a footing with lawyers, physicians, etc. They ought therefore to possess the same rights.”
And Jefferson rejoiced at Rev. William Wood’s election over Peter Carr in a letter to John W. Eppes in 1799. He also personally appointed clergy while President to various posts in the government and as federal judges, etc.
The modern stereotype of Jefferson as a clergyman-hater, even of those ministers involved in politics, is not true.
Note: the image is from the University of Virginia, that Jefferson helped play a key role in founding. Photo by Jerry Newcombe
 Subscription to Support a Clergyman in Charlottesville, February 1777, www.founders.archives.gov.
 Testimonial for Rev. Charles Clay, August 15, 1779, www.founders.archives.gov.
 “From Thomas Jefferson to John Wayles Eppes, December 21, 1799,” www.founders.archives.gov .