In one of the essays in his collection The Trail of the Dinosaur, Arthur Koestler makes the point that many of the historical dilemmas or controversies that once seemed most insoluble were eventually overcome—not because one side or the other at some point "won" the argument—but simply because new problems emerged that made the whole previous debate seem silly.
The Crusades didn't end because Christianity "beat" Islam or vice versa. So too, Catholics and Protestants never did manage to exterminate one another in Europe's wars of religion—much as they tried. Instead, in both cases, the two sides first fought each other to a stalemate. And it seemed there was no possible exit. But then, new social circumstances arose that made the whole fight seem boring and irrelevant.