R. C. and R Hampton:

I think you both might be right. It makes sense that the phrase “monkish superstition” was meant to describe teachings of (primarily Protestant) religious leaders in America. But the reason he that called it “monkish” was likely to insinuate that their teachings were similar to those of their despised rivals in the Roman Catholic Church. Back then, Catholic and Protestant clergy hated each other at least as much as they hated atheists and deists, so if Jefferson really wanted to get their goat, he would compare them to each other.