I dunno if you noticed, but in the real world, when a genocidal maniac is held under arrest for his trial, it doesn't happen for a long time and if it does, it generally doesn't have a particularly climactic ending.
Polpot, for example. I know Saddam had his trial in Iraq, but nothing really happened.
To paraphrase Eddie Izzard, an English stand-up comedian: "When you kill a handful of people, you're a murderer and that's really bad. But when you kill thousands of people, we don't know how to deal with it. We just look at them and go, 'er... well done!'"
Granted, Banner was put on trial and had a big dramatic ending, but he was essentially treated as a serial killer (just with a ludicrously high body count to fit the superhero genre) - he had no society or backers, he acted alone.
Magneto is essentially, a head of state. First they have to get the information, and proof to put him on trial, then there's the complexities of the proceedings - he won't be put on trial because the world just doesn't know how to handle a man of that power and influence. The justice system is not equipped to deal with men such as him.