I can't really see any easy explanation for it other than simple bigotry. Most Pagans strongly disagree with typical Christian concepts like Original Sin, but Christopagans may or may not even hold to those concepts, so that alone can't explain it. What it comes down to, I think, is the “Burning Times” origin myth.
The witch hunts had nothing at all to do with Paganism, except perhaps in a few localized and isolated examples. There was no organized remnant of Paganism left in Europe by the time of the witch trials, and the idea that the witches were Pagans is a complete fiction. The “Burning Times” are an imaginary persecution. The witch trials really happened, but they were a matter of mass hysteria and moral panic, not an organized attempt to suppress Paganism. Therefore, Pagans who hate Christianity because of the “Burning Times” are angry about something that never even happened in the first place.
A thousand years or so before the witch trials, there were certainly cases of Christians persecuting Pagans. And five hundred years before that, the Pagans were persecuting the Christians. Hating Christians because of what the church did to Pagans a thousand years ago is pure insanity. It would be like Christians hating Pagans because of Nero and his lions.
When Christian bigots try to suppress Paganism in the modern world, they must be strongly resisted. But when Pagan bigots respond by hating all Christians across the board, they only prove that the real problem has nothing to do with Christianity. It has to do with human nature.