In the movie they are "brothers" ,which does not mean that they share a biological mom and dad.
Magneto ,in most vrs. of the character, truely believes that armed conflict between the bulk of humanity and mutants will happen. He also refuses to allow his "people" to be slaughtered again, not when he has the power to stop it. He wants to "take over the world and put mutants in charge" because he truely believes that there is no other way. And yes he has done things that are horrible to that end, becuase he thinks that voilence is the only way humans can be communicated with. I wouldn't call him evil but ... he fudges the line. It depends if the action or the intent behind the actions is more important to you for determineing what is evil.
Megs on the other hand wants to become the ruler of the universe by any means required (short answer). I would say he is evil.
Oddly I consider some of Magneto's followers evil and some of Megatron's not.