The Punisher is at base an extremely problematic character. Or rather - let me phrase this correctly - he's an extremely problematic character in the context of general-audience action-adventure franchises. At base, there's no getting away from the fact that he's essentially the world's greatest serial killer. If you have the Punisher as a recurring character and not merely a one-off villain, it naturally follows that he kills a lot of people. That's what he exists to do. Kill people. It's kind of their in the name - Spider-Man is spidery, Superman is super, and the Punisher - well - he punishes people.
And it's worth keeping in mind, in an era where "mature readers" has essentially become the baseline for all mainstream comics not released under the "Marvel Adventures" or "Johnny DC" labels, that until the year 2000 every single Punisher comic ever printed was published with the Comics Code seal of approval. There were isolated graphic novels and "Prestige Format" stories, but every single issue of the character's regular series - and there were many hundreds of them - was theoretically safe for children. In practice this didn't work out so well - by the time the Punisher had become such an incredibly popular character, the Code had already become toothless in many ways. The Punisher was one of the most violent comics on the stands, and the very basic premise of the character as anything other than - repeat after me - a villain (which is essentially what the character had been, a few gritty appearances in Marvel's short-lived black & white magazines notwithstanding), sort of went against the grain of the entire Marvel Universe. Or at least the conception of Marvel as a publishing company whose entire mainline was theoretically fit for kids aged 8 to 80.
So despite the character's unquestioned popularity, the whole situation made for a pretty rough fit. After the success of Marvel's first Secret Wars series, Mike Zeck's next assignment was the first Punisher five-issue mini-series, with Steven Grant (although Zeck and Grant only did the first four, for complicated and unfortunate reasons), pretty much the diametric opposite from the space-based cosmic opera of Jim Shooter's Secret Wars. The series was, by all reports, a surprise hit - Marvel hadn't expected it to sell so well, but as soon as it did they rushed an ongoing into production, on which Mike Baron logged a successful run over the course of the next five years or so (give or take a few fill-ins). Grant and Baron's take on the character was pretty much the only feasible take given the context, and became the default mode for his next decade of adventures - less focus on the insane psycho-killer aspect of the Punisher's character, more on the boys'-adventure, PG-13 Rambo stuff. Sort of like, say, a Mack Bolan novel aimed at a slightly younger audience. However: the Punisher did not - and could not - have much in the way of depth (at least inasmuch as it was traditionally defined in the post-Chris Claremont, constantly dynamic Marvel Universe), because his status quo had to remain unchanged.
The Punisher himself, if not exactly a good vehicle for ongoing soap opera (and every attempt at grafting any kind of supporting cast or soap opera background died on the vine), was great for isolated adventure stories. So in essence, the Punisher as a character was very similar in conception to how super-hero comics had been pre-1961: episodic, static. Nothing ever really changed for the Punisher. He was stuck in his milieu, and nothing could change this, because to a large degree changing the Punisher's milieu would have meant changing the character. Give him a supporting cast (besides fellow vigilante Microchip), soap opera shenanigans, any kind of super-hero trappings, and you butt head-first against the fact that the character is a ruthless serial killer. Keep him isolated, keep him occupied. The character, because of his near-perfect featurelessness, has been used to great purpose by Garth Ennis as a vehicle for both dark comedy and black morality tales - but neither option was really available to the folks writing the Punisher back in the late 80s and early 90s. So the Punisher was one of the few Marvel characters for whom nothing ever seemed to change - you could pick up any random issue and the story would be the same, just the scenery would change.
While nothing ever really changes in comics, the illusion of change keeps the cash registers ringing: Spider-Man remains Spider-Man, but good writers fill his life with so many constantly-changing variables that it can seem new, especially if you haven't already read hundreds of Spider-comics. But eventually everyone (or most people) realize that superhero comics are by nature unable to change. Most people either learn to appreciate serial comics differently than when they were twelve - i.e., by appreciating the good and bad aspects of craftsmanship and storytelling that individual talents bring to the table - or they get stuck in perpetual adolescence, demanding increasingly high stakes for the illusion of change they crave to keep the reading experience fresh and interesting. As the economic disaster of 90s comic publishing hit the realities of an aging, increasingly hard-core fan base, it became that much harder for the Punisher to remain interesting.
If the illusion of change - the suspension of disbelief necessary for older fans eager to believe that they are not wasting their time on the same stories they've read a thousand times before - was difficult to maintain in comparatively rich and diverse characters such as Superman and Spider-Man, imagine how tricky it would be for a character like the Punisher. When sales started to lag, and attempts were made to shake up the status quo (already de rigeur in the 1990s, when seemingly every major character experienced major upheaval in an attempt to ape the success of Superman's "death"), the Punisher took it harder than anyone could have expected. By trying to change the character's milieu, they had done seemingly irreparable harm to the character's appeal.