Yesterday was Jefferson's birthday. On his tombstone he prescribed recognition not of his presidency but of two things he authored, one stating in its preamble, "... That to compel a man to furnish contributions of money for the propagation of opinions, which he disbelieves is sinful and tyrannical; ... That our civil rights have no dependence on our religious opinions any more than our opinions in physics or geometry, ...".

The preamble was quite longer than the statute; reprinted in total at Wikipedia.

See: Google websearch = Virginia Statute for Religious Freedom

While lacking any proof either way whether the question of taxing churches and their property was an issue of Jefferson's time, or whether he had any opinion, it seems he would have reasoned that the property is no different than if owned by any other person or economic venture besides a church. That a church had no inherent merit to special tax treatment, and that to accord it special treatment was a questionable judgment of human beings, not a divine mandate. Happy birthday, sir.