I think a lot of the blame has to go to the Garden of Eden version of human history. (And not just the fundamentalist version; there are plenty of secular belief systems which have descended with modification from the original.) The belief that once upon a time we were living in Paradise (no, it was a bloody, brutal world long before humans ever existed), that we were kicked out of it due to some easily identifiable villain, and if we can only (to use the biblical language) utterly destroy the Evil side, the Good side will live happily ever after. The would-be purifiers have tried to make it work so many times with every version of evildoer imaginable, and not once has it delivered the promised results. So how does that worldview remain so enormously popular? Maybe TRUE "Thou shalt utterly destroy them" has never been tried?