In the last Squadron Supreme series they kill the Sub-Mariner for a list of crimes going back 80 years, then the original Invaders feel like they have to do something about his death because he was their friend. 
Honestly even with diplomatic immunity you’ve got to wonder why SHIELD didn’t go after him years ago.
Maybe this is what gdave was referencing (I admit to being not up on my Marvel universe knowledge), but this question is why the allegory in the first few X-Men movies (and maybe beyond; I didn’t keep up with them) always rang a little false to me.
The amount of death and destruction caused by “supers” just couldn’t/wouldn’t be tolerated in the real world.
If you need the “good” ones to protect you from the “bad” ones then I guess you figure out how to make it work, but clearly the safest option for mankind is to neutralize all the supers.
Do you arrest Superman? Well, if he’s the only thing standing between us and destruction, then no, he gets to live a consequence-free life for the sake of humanity. Any harmful acts he makes, intentional or not, are the tribute we pay for survival.
If, however, we don’t need him to keep us alive, then arrest that fucker and throw away the key.
To protect their families and loved ones.
I’d be willing to cut superheroes some more slack on an individual case-by-case basis. If a superhero is indeed doing the world a great deal of good, such as preventing a 9/11 here and there, stopping pandemics, etc., then I am OK with him getting away with some minor illegal stuff, such as some theft or whatever. He can’t go around murdering people he dislikes, that won’t do. But I am willing to cut him more legal slack than the average person.