You are probably right that it is not a lack of understanding but a particularly devious form of mockery. Keillor spoke at my college baccalaureate. He told this story of going to a church that put the "fun" back in "fundamentalist" and how one Sunday morning the preacher prayed over him, embracing him, and he smelt liquor on the man's breath. "You haven't lived," Keillor said "until you've been prayed for by a drunken preacher."
While I'll agree that we're all fallen, preachers and everyone else, I seem to remember that Keillor actually grew up Methodist. Unless there are pockets of Methodists who put the fun back in fundamentalist and rant about fire and brimstone (and not the church soft ball league), he made the story up out of whole cloth.
A satirist has typical enemies on both sides.