Deadpool is often portrayed as this. Even with his rampant insanity, the guy is shown to ultimately mean well and he frequently tries to improve himself. When he ended up in X-Force, he quickly proved to be the most moral member of the team who called out the rest of the team whenever they did something that crossed the line. In fact, it's increasingly strongly suggested that Deadpool acts like a jerk towards others simply because he's afraid of being rejected.
Reed Richards, who acts like an arrogant, insensitive dick most of the time, but loves his children, wife and adoptive family dearly, has an extremely strong and idealistic moral compass, and suffers a great deal of guilt over the accident that ruined the Four's normal lives.
For that matter there's his brother-in-law Johnny Storm, who can more often than not be a cocky, immature jackass. But he always stands by his friends and loved ones and will give his all fighting for the greater good.
Doctor Doom loves pushing people around and launching attacks against his enemies (namely everybody who's not him) but has warmth for his citizenry, particularly the children of Latveria. In a truly shocking moment, he forgave past grudges and aided the Invisible Woman with her second birth, saving both Sue and her baby from certain death. As such, the daughter, Valeria, is held as an endeared one under his personal protection and allowed unrestricted audience, while the child returns his affection and refers to him informally as Uncle Doom. Awwwwww. (Warning: This is most definitely a Depending on the Writer quality.)
Reed Richards from Ultimate Fantastic Four means well... sort of, but there are moments where he's incredibly arrogant and bad tempered. Becomes a full on Jerk with a Heart of Jerk when he turns evil because he felt being good was holding him back.
Tony Stark alias Iron Manis this trope IN A CAVE! WITH A BOX OF SCRAPS!!! This applies to both his comics incarnation as well as how he's treated in films. Notably, he only really developed the heart of gold after the accident that made him Iron Man; before that, it was in there somewhere, but not so you'd notice.
Namor is at best a gigantic asshole. But he truly does care for his friends, such as Bucky Barnes and Steve Rogers, and will do what is necessary to protect his people. He also flooded Wakanda, and although he was kinda possessed by the Phoenix Force, he later confesses that the only thing he regrets is that so many Wakandans lived, and he wasn't possessed when he said that. And that's after he pretty much told Thanos to attack Wakanda.
Spider-Man: J. Jonah Jameson. Sure, he's short-tempered, tight-fisted, and an often obnoxious loudmouth, but he's also been shown as a tireless crusader supporting everything from labor union rights to mutant rights, going after organized crime figures and corrupt politicians despite repeated attempts on his life, and discreetly supporting various charities and social projects, and even hiring a good lawyer for Peter Parker when Parker was falsely accused of murder. He's been pretty much consistently portrayed as a social liberal whose ideals are wrapped in civil liberty and constitutional rights. despite the fact that he's a mean-spirited douche to the people around him.
In the arc where Spider-Man publicly unmasked himself as Peter Parker, Jameson went so far as to refer to Parker as being like a son to him, and that he had always regarded Parker as the "last honest guy in town". What does Jameson do next? Turns around and sues the crap out of Parker for misrepresentation. Of course, he wasn't entirely unjustified in doing this; he was also later confronted by other characters about how much of a jerk he'd been to Spider-Man / Peter over the years.
It should also be noted that Jameson's character is interpreted drastically differently, Depending on the Writer. Some writers really tend to push the "heart of gold" aspect, whereas others still prefer to present him as a genuine Jerkass, ignoring any character development to the contrary by other writers. (This usually coincides with alternating interpretations of Jameson as a genuinely competent newspaper publisher and an angry tabloid publisher with an agenda. The latter version is occasionally characterized as clueless and outright sociopathic, too, whereas the former version sometimes borders on hidden philanthropist. It's really inconsistent, to say the least.)
It should be noted that during Stan Lee's run on Spider-Man Jameson is always a JerkassScrooge who feels that appearing to have a heart of gold is the best way to make money.
Mainly though, the character seems to be kind of like Spider from Transmetropolitan. He's a complete asswipe, no doubt, but he surely is also a kind person at heart and has shown this on several occasions. For example he genuinely cares about honesty, integrity and civil liberties and can be quite nice (or at least, less caustic) to his friends, like Peter or his employees, despite being a sarcastic jerk.
JJ was once offered a deal: if he stopped bashing Spidey every time he needed an editorial, he'd get an exclusivity deal with the New Avengers. He even got to hear Captain Fucking America tell him Spidey was a hero rather than a monster. His response? After shaking hands on the deal, he promptly went back to not only committing libel, but making accusations of bribery and digging up things like "wanted murderer" (Wolverine), "terrorist" (Spider-Woman) and "convicted drug dealer" (Luke Cage, who was framed and exonerated).
These inconsistencies are avoided by the Ultimate Universe J. Jonah Jameson (probably because the only writer was Bendis). He embodies this trope completely. Three examples stick out - firstly, after firing Peter in a temper tantrum, he comes to the kid's house and opens up to him about his son dying, before offering to give him his job back and allowing him to start shadowing Ben Urich so he can get a taste for real journalism. The second is him doing a Heel–Face Turn on the whole Spider-Man thing after the Ultimatum arc when it's not certain if Spidey survived, and writing a heartfelt public apology/obituary for the webslinger. Lastly, he eventually discovers Peter's secret identity and his first reaction is to offer him money. He says he'll pay for Parker's entire college education on the basis that "I'm a rich man, I'd hardly notice."
In Marvel Versus DC, when it looks like The End of the World as We Know It, Spidey asks Jameson if he has any last digs to get in. Jonah responds "For what it's worth, I'm sorry", to which Peter can only say a quiet "Oh."
In the storyline The Death of Jean DeWolff, Jameson responds to a question about whether he believes Spider-Man deserves to die with "Hitler deserved to die, so do assassins, cop killers, scum like that. Whatever else he is, Spider-Man is not one of those."
In Alias Jessica humiliates him when he hires her to find out Spider-Man's identity while badmouthing both superheroes and private investigators (she spends a full month doing charity work and billing it to the Daily Bugle). Even his own employees start complaining about what a dick he is about it. But then he and his wife hired her to find Mattie Franklin, their missing adopted daughter (the latest iteration of Spider-Woman), whom Jameson deeply cares about. When they meet with her, his wife explains that Jameson has many issues that mostly stop him publicly showing a caring side, mostly regarding his son. After adopting Mattie, he tried making up for his failures with his son by being a good father to her. This is why her troubles hurt him so deeply, since he feels like he's failed again. Fast forward to the last pages of Alias and Luke is seen complaining that Jessica now seems to be the only super Jameson will write positive headlines about.
This is a frequent characterization of Wolverine. He's always talking back to authority figures, even if he agrees with their choices, will regularly get into fight with friends with next to no provocation (at one point trying to kill Colossus for daring to save his life) and is unapologetic in his killing, few cases aside, because he thinks, no matter what people say, it's what they want from him. However, he is deeply loyal to his friends, and will go out of his way to get his own hands dirty so no one else has to.
Northstar tends to be something of an acerbic arrogant bitch to everyone around him... except his Tennessee Williams-style mentally ill sister (well, most of the time, anyway) and especially his deceased adopted infant daughter, Joanne Beaubier.
In his darker characterization Cyclops is this. In recent times he formed a hit squad of the more sociopathic members of the X-Men to kill the X-Men's greatest enemies. Before that he had a psychic affair on his wife who died later (Though he was going through a deep emotional breakdown and he was manipulated into doing so) and before that abandoned his wife and son to go to his ex girlfriend (but at the same time he was emotionally conflicted, tried to make it up and felt really guilty afterwards as well as possibly being manipulated into doing that as well). However, he only formed the hit squad in the first place to protect mutants from their most dangerous enemies while they were on the verge of extinction where all it would take is the slightest super weapon to destroy them. In Deadpool X Marks The Spot he sends Wolverine to kill Deadpool, but only because he risked making the X-Men look like monsters and earlier comforted Mercury when her father was being a dick. And while he at times is displayed as a cold emotionless leader, he was visibly upset when Thunderbird (A real Jerkass) died despite him being powerless to stop it from happening, as well as feeling guilty that he allowed Kitty to get trapped in her ghost state/a giant bullet.
Nate Grey takes after his father in this regard, being brusque, paranoid (and given that he grew up in one of the iconic Marvel dystopias, the Age Of Apocalpyse, and practically everyone he met wanted to kill him or use him, it's not hard to see why), and fairly merciless when people crossed him. He also had a more hair-trigger version of his mother's famous temper. However, he also shared his father's Adorkable traits and his mother's All-Loving Hero nature, sincerely trying to help people wherever he went, despite the fact that his powers were killing him and his heroics usually attracted more screams than acclamation, being genuinely delighted during his time as New York's 'street messiah' because he could help people. No matter how many times both Maddie and Threnody either ditched him or tried to use him, he tried to help them (if with some suspicion) - and he had a decided soft spot for children. Even after his Face–Heel Turn to well-meaningAnti-Villain, where he casually demolished entire teams of X-Men, he didn't raise a hand to the Young X-Men and happily and honestly answered their questions.
Emma Frost also tends to be this. Despite being the bitch she is, she cares about the mutant race, her friends, her students and Cyclops.
Quentin Quire has become one following his Heel–Face Turn.
Hellion as well. He's a smug, arrogant, self-entitled prick to most everyone, but also fiercely loyal to and protective of his friends. Seeing many of them killed during Stryker's attacks against the school would affect him very deeply.
Captain America. Flaws or not, he's still Captain freakin' America. He's fairly forward thinking for his time even if he does retain some misogyny, and though he doesn't show it as much and can come off as very cynical, he does share his 616 counterpart's strong sense of idealism and heroism. Spider-Man's death certainly helped tone down his jerkass side.
Monica Chang. She may be the Alpha Bitch of the team, but she's also a loving mother, passionate about defending her country, and worries about her teammates in fights.
