Sure there's a difference. Bruce Willis' character in UNBREAKABLE and Duncan MacLeod in HIGHLANDER are "protagonists with super powers," but neither one is a superhero.
su·per·hero
Pronunciation: -"hir-(")O, -"hE-(")rO
Function: noun
: a fictional hero having extraordinary or superhuman powers; also : an exceptionally skillful or successful person
A hero, only moreso. Thus, Superman is a superhero -- but so is Batman, so is Captain America.
I'm not too familiar with the Question so I can't make any kind of judgement on whether he'd be considered a superhero or not. As for the Punisher, wouldn't he be considered a vigilante instead of a superhero? I mean, he is taking the law into his own hands by acting as judge, jury and executioner.
1 a : a mythological or legendary figure often of divine descent endowed with great strength or ability b : an illustrious warrior c : a man admired for his achievements and noble qualities d : one that shows great courage
2 a : the principal male character in a literary or dramatic work b : the central figure in an event, period, or movement
Would the Punisher be a superhero because he's "an illusturious warrior"?
The Punisher was an out and out nutcase, some could argue that he was still a good guy because he only targeted criminals - however he shot someone in the knees for jaywalking - some criminal!*
* However this was later re-conted out by saying that he was acting under the influence of drugs.
"Hero" is often used of a main character whether or not he has any heroic characteristics. "Superhero" was traditionally used of a character who has heroic characteristics, in opposition to "supervillain," not just of a main character with superpowers.
But in those days the idea of creating a story of a superpowered character without heroic characteristics was pretty much unimaginable. I'd say that by the mid-80s expanded the definition of the category to include all superpowered characters who in any way fought crime whether or not they were particularly heroic. (The issue of whether or not they were main protagonists in a specific story isn't germaine.)
In his first appearance Punisher was not an all out villain. He was misled by the Jackal into thinking Spider-Man was responsible for Gwen Stacy's death. Throughout the issue he also showed a disdain for the Jackal and layed off Spider-Man when he found out he had been misled. He was not portrayed as a psycho in his first appearance. While Punisher certainly scrapes the bottom of the barrel I think he still is on the hero side, but just barely.
I'd say a "hero" is someone who does the right thing for the right reason.
What we tend to see in excess in comics these days are antiheroes -- people who do the right thing for the wrong reason, or the wrong thing for the right reason.