@ Sephiroth7734:
I do think you may have misunderstood my point.
Understanding why someone does something doesn't mean agreeing with it or condoning it. I can (on an abstract and logical level) understand why a certain serial killer murders women. That doesn't mean that I think murdering women is okay, nor that I'll go out tomorrow and murder women.
As such, while I understand the reason behind a villain's action, it doesn't make me think he's suddenly not evil or that what he's doing is okay. He's motivation doesn't excuse his actions.
Good and evil aren't distinguished just by motivation, but also in combination with a choice of action.
Say there's a village that has a rat problem. Joe and Jim want to help rid the village of the rats and make sure that the villagers don't need anything else.
-Joe goes into every house, defeats each rat one by one. He then completes several tasks for the villagers until they feel happy. After the thanks, he merrily goes his way.
-Jim sets fire to the village. This gets rid of all the rats, as well as the villagers needing anything else - they don't since they're dead.
They both had the same motivation, yet one of them would be called a hero, while the other an evil villain.
Morality kicks in here when their individual actions are judged and categorized. As human beings, we are constantly naming, identifying and categorizing the world we live in. And because we're capable of abstract thought, we can name, identify and categorize things that we can't perceive through the 5 senses. The principle of morality is just a way to categorize attitude, behavior, thought and action into two areas: good and bad.
I think everyone will agree that the morality of individual actions is a gray area. Whether things are considered morally acceptable depends on the society (i.e. culture) and the circumstances.
Cannibalism, for example, is considered morally wrong in North America, yet there are tribes in Africa where it's perfectly acceptable. Does that mean that one of them is wrong?
No. It simply means that the societal rules are different, and thus morality is different.
Murder is considered morally undesirable - as demonstrated by the fact that murderers are thrown in prison or executed (depending on the state). However, if you murder someone in self-defense, you walk free. You don't spend decades in jail because your actions were judged to be acceptable within the society.
Because of this, I can see how tempting it must be to say that any action with proper motivation can then be seen as morally acceptable (i.e. good). However, the key factor here is that society is the judge in what's moral and what isn't. It's not a matter of just individual opinion.
A evil villain is an evil villain not simply because of his/her motivations, but because the choices he/she makes are not wanted by the majority of the society they live in - even if their reasoning is understood. They're categorized as evil even if the villain him/herself doesn't think they're wrong. The opinion of the majority is the key.
Taken individually and in different circumstances, the motivation and the action of a villain might be morally acceptable. Wanting a pure world (for example) is an acceptable motivation for a priest to go and preach to the village. Even something as extreme as torching an entire village is acceptable if the villagers are mutant zombies bent on infecting and eating everyone around them.
However, if what the villain is doing or the reason they're doing it are not acceptable, they're quite simply evil - regardless of how they feel about it.