Seems to me there are two possibile explanations for why people persecute others for their beliefs:
1) A genuine disagreement over the issues, a belief that such people are morally reprehensible and/or dangerous for holding them.
2) A cynical desire to maintain their power and position by stifling opinions that draw their own authority into question.
The first is possible, I suppose. But I lean toward the second, because it seems to me that persecution occurs in all realms of human intercourse, both religious and secular -- but is rarely led by people who don't have an economic and/or political stake in the outcome.
Don't get me wrong -- I'm sure there are many troops in these wars who genuinely believe the enemy is bad -- but it seems to me they're just pawns who have been deceived and emotionally manipulated by leaders who always have a personal stake in the outcome.
Consider the Catholic Authorities trying to maintain their hold on Europe through the inquisition. Given the unfalsifiable nature of their claim to authority, could they afford an alternative whose claims were equally unfalsifiable drawing their own into question?
Or evolutionary biologists insisting so rabidly that no alternative is worthy of consideration. What would happen to the funding for their research if it were acknowledged that their theories are absurd?
Or Republicans and Democrats (whose policies are often indistinguishable) using the rhetoric of ideology and morality, and then turning around when in power to do things totally counter to what they said. What would happen to their power and ability to draw contributions and alter the law to benefit themselves and their friends if the other side's moralizing went unanswered?
Or Muslim clerical authorities who use law to stifle religious dissent. What happens to the religious authorities' power if others are free to question it?
And on and on and on ...
It occurs to me that if one attempts to take on these forces through ideology -- through arguing about ideas -- one is simply wasting one's time; because the oppression is not itself about ideas -- it's about the power and authority of those whose ideas are being questioned.