Okay, let me try to break down why people tend to see the german actions in World War II as evil, but why they really weren't at the time.
1. War of Aggression
They started it. At least from our perspective. To them a lot of the attacks on other countries were in the area of payback for World War I (of which they had wrongly been blamed for).
Once they got their tanks rolling and were on the winning streak that whole World-Conquest-Idea hatched, It was just offering itself at the time since the Blitzkrieg was revolutionizing warfare.
And even if all their attacks were Wars of Aggression, you really can't say these are evil. Sure it's not really polite, but it has been done at any point in history and was not specifically illegal at the time. (All the international laws that condem this kind of warfare have been invented after WWII. And even today they can be bent. (See the war against Terrorism)).
2. Genocide
The idea of eugenics and racial purity was a worldwide idea in the 19. and 19. centuries. Every nation had eugenical institutions and representants. The germans just took it to industrial perfection, just as they did at the time with everything else.
It may be hard to swallow that pill, but germany was the technological superpower of it's time at the start of WWII. They really just finished the trains of thoughts other people had started, pretty much like they did with the developement of the Panzer.
And then of course there is the fact that the Allies commited enough shit that came close to the Konzentrationslagern themselves. Japanes Internment-Camps anyone?
So in summary: Yes, from our perspective these acts were definately evil. But you can not handle history like that, or it turns into 5000 years of evil. The germans firmly believed that they did the world a favor by killing the jews. While this is a demented point of view, to improve the world for the good of all humanity (what they see as humanity anyway), is generally not the mindset of a villain.