Well, one thing I feel is that he may have something against the world, but not necessarily humans being evil. Oh sure, the characters may have less than honorable motivations but you still have people fighting for the sake of others and making sacrifices so this can happen. If people are capable of doing this in a cynical world, then perhaps humans really aren't such assholes after all, even if some decide to not care.
There's really no one that's really portrayed as incurably "evil" and a bastard in Madoka though Kyoko does cross the line, except the forces of the universe would be antagonistic to humankind-- personified in Kyubey. I'm sure there's Puella Magi that did use their powers for those means, but they aren't brought up...
Fate/Zero's lines are far more blurry, with even our protagonists commuting seemingly terrible acts. But there are still those that help another and not just kill for the lulz. It's war though...
Morality isn't always so clearcut when taken into context. It's why stories like the UC Gundam ones are so distinct; the opposing sides aren't always so polarized, and there are honorable and good people on both, who had just the misfortune of being on the wrong side. I tend to like stories like those as opposed to ones where; well... let's not bring them up anymore or I'll go bash a certain writer again.
But like I've said before; sometimes a failed protagonist or even an antagonist would have made a good hero in another story-- that is the sign of a good character.