He doesn't. He avoids them at almost all costs. Just because he has fought them, that doesn't make it a regular occurrence.
Here's a list of his appearances:
http://www.comicbookdb.com/character.php?ID=161
Why don't you go tabulate a list of all the times he goes against super-villains. It will be dwarfed by the non-powered list.
Meanwhile, Batman figures out how to kill Darkseid.
Seriously, I know the Punisher fits the NRA's wet dream and he is remarkably skilled but he is by no means the most dangerous non-powered human in the Marvel Universe. Being willing to kill does not automatically make you more dangerous. It does attract the attention of people who wish you wouldn't.