Everyone gets that he represents the brutality of the justice system. It's just that most people in the justice system don't see his behavior as a fault or criticism; just reality.
Like a lot of people, you have an idea of the character which is not the definitive version of the character.
If you read the Punisher and you come away from it thinking that vigilantism, murder and so forth is good then there is probably something very wrong with you.
To your credit, as a non-Punisher patron of geek arts, you're probably right. The spirit of the original comics is likely expressing a deeper message than most people could understand from a cursory glance and watching one of the dumbed-down movies.
To your discredit, the population at large generates a mythos that transcends the character and strips away all sense of subtlety. To anyone who doesn't know the comics intimately, The Punisher is a guy who's like Batman with more brutality.
And, at the risk of redundancy, I'm convinced this is true of pretty much any character, fictional or non-: caricaturization of their greatest qualities, then memorialized as a god of [subject matter expertise]. The _only_ time I've ever seen a deviation from this is when a character is hard to place because they're all over the map (e.g., Ben Franklin, Christopher Lee).
I mean, The Author Is Dead; this is a fair interpretation. But I'm skeptical that the kinds of police who put a Punisher skull on their uniforms feel this is some kind of Full-Metal-Jacket-duality-of-man commentary as opposed to just fantasizing about murdering [who they imagine to be] criminals.
I daresay "desirable".
https://en.wikipedia.org/wiki/Thin_blue_line#Symbols_and_var...
Zack de la Rocha and the others don't typically receive the same criticisms unless their actions are lumped in with Morello's under the banner of "RatM did X".