Hmm. R Hampton says, “Jefferson was referring primarily to Protestants who both hated and feared Jefferson (especially in the run-up to the 1800 election)….”

This may very well be the case. But I hope I can be pardoned for thinking that the phrase “monkish ignorance and superstition” had more of an anti-Catholic ring to it. (I haven’t encountered many Protestant Monks, though I suppose there are some.)