Cpt. Dahl from Air Force Blues. At least, when he gets into serious "Danger Zone" mode.
Ito, the God of Trust and Betrayal from A Moment Of Peace, steals dreams and crushes hopes for a living, and has prosthetic hands forged from moments of despair by crows that grew hands to strangle people. Despite all this, he seems to be a nice guy when you get to know him.
Paulo from Bittersweet Candy Bowl; while he often acts like a jerk, and hits on girls, deep down inside he is a very nice young man who does care about his friends, and who doesn't need to be thanked for his help.
Leodegrance from The Bug Pond is often portrayed as a vain idiot, but he is shown to genuinely care about the wellbeing of others and is eager to help in most situations.
The Klegdixal ambassador from the Gallimaufry arc of Buck Godot: Zap Gun for Hire, and possibly the Klegs as a whole. The way the ambassador tells it, the Beemahs are their albatross, and they desperately want to fix the mistakes they made with the poor fuzzy little weapons.
Amon Thorn from Cwynhild's Loom is typically rude and comes across as selfish, but in reality he cares a great deal about the Valkyries and is risking everything to help them.
Abel from Dan and Mab's Furry Adventures . Though sometimes it's hard to tell whether he's a Jerk with a Heart of Gold or just a plain ol' jerk. Also, Wildy; she's the kind of tomboy whose idea of caring sometimes takes the form of "only I get to beat up my friends, damn it!" ... but it's there nonetheless.
Netta from DDG usually spends her time thinking up fresh torments for Zip, but can be capable of the occasional sweet gesture.
Melissa of Eerie Cuties and Magick Chicks. She was an Alpha Bitch in Charybdis Heights, aspires to the same in Artemis Academy, can be very mean, but more irritable than vicious. When her goddess goes on a flipped-out rampage, her thoughts, in order of appearance are — "That wand is the key to my popularity! I have to get to it before Hekate's whatevers destroy it! Or that dumb blond girl gets hurt, I guess. Or... or Faith." — given that Faith is the one she aims to depose as the Queen Bee, already tried to Mind Rape her and this very trouble started due to Faith's games.
Trawn from Electric Wonderland can occasionally seem single-minded and forceful in her movement for her newspaper's success, but she does show sympathy for Aerynn (due to her rejections from society) and Lululu (due to her household's state of poverty).
Susan adopts the angry Straw Feminist role, but she's both smarter and nicer than that. So when something touches her where this convenient mask is too stretched, the next moment it's torn and you can see the real Susan (a cynical Deadpan Snarker, but not without compassion), while jerks still face "The HammerQueen".
Bob of Emergency Exit is surprised to find out other people see him as this: 'jerk' because of his poor social skills and unwillingness to show affection, 'heart of gold' because he genuinely does care for his friends.
Equius Zahhak may be a racist thug, but after Gamzee goes Ax-Crazy, the first thing he does before heading out to confront him is send Nepeta to safety. After the two of them had spend some time talking about their feelings in the robot pile after Aradia's explosion.
Dave fits this category quite often, too. Obsessed with coolness, relentlessly stoic, obsessed with doing everything ironic and overly fond of pissing off the trolls, but his letter to John gives away a lot of his actual personality, refuses to let Rose sacrifice herself, and it's likely his fondness of irony is used an as excuse not to admit he gives a damn. He also occasionally lets something slip without checking he's got his irony up.
As of later comics, the 'heart of gold' part becomes very obvious with Karkat. He takes his role as "Team Leader" extremely seriously and feels immense guilt over not being able to lead his team to victory (despite that arguably not really being his fault), as well as the fact that he unknowingly sabotaged the Kids' game session due to his own mistakes. He is shown to care deeply about his friends underneath all the insults, and he will reign himself in and apologize if he ever crosses a line with his vitriol.
Honestly, damn near everyone in the comic.
Jamie from Khaos Komix is typically depicted as a grouchy, mean, homophobic Jerk Ass. In his girlfriend Charlie's story he's shown to be quite polite and nice. It appears that something happened when he was younger that sparked his mean behavior.
Mora and Rachael from Las Lindas. The writer tries to portray Miles as one, but most consider him just a regular jerk.
Matt of Ménage à 3 is widely regarded as a jerkass for his repeated, compulsive sexual infidelities — but perhaps more by readers than by anyone in the comic. The fact is, in any matter that doesn't depend on sexual fidelity, he seems to be a good, reliable, helpful friend (if a little bit snobbish about people who aren't as attractive as himself). Even an ex-girlfriend who suffered from his lying and cheating will turn to him for advice — and he'll take a break from sex with a lingerie model to provide it.
morphE features Billy Thatcher a chess champion with no patience for ignorance or people holding him back. He has cowardly tendancies and is quick to insult others. However he does fill a leaderly role in the seedling group and is quick to protect the youngest member and scold anyone who carelessly hurts their feelings.
Varsuuvius occasionally has a bit of this. V is pompous, arrogant, pedantic, looks down on non-elves and less intelligent people with equal scorn, genuinely hates at least one teammate, and generally doesn't seem to be very motivated to save the world. Even so, there have been moments of V genuinely caring for teammates, notably Haley. The one teammate s/he hates is a Token Evil Teammate. The character arc where V makes a Deal with the Devil to save hir family from a vengeful Black Dragon takes this Up to Eleven.
Though his group finds him unpleasant and cranky, Rocky from Our Little Adventure isn't such a bad guy.
To varying degrees, almost all of the major male characters in Out There (the exceptions being John and Chuck). James is selfish and abrasive, arrogant, constantly borrowing money without paying it back; he also volunteers at a homeless shelter. Clayton is surly, has been known to steal alcohol from his favorite bar, and is constantly seen mooching off of others; but he refused to take advantage of Miriam when she was drunk. Steven and Rod are unrepentant philanderers, but are generally loyal and respectful towards their ex-flame-cum-best-friends (Sherry and Araceli, respectively). Wally is a repentant (and former) philanderer. Considering the fact the main character, Miriam, has enough flaws to fill a book (while remaining unerringly sympathetic) Out There seems to be a world where everyone is a little bad, but nobody is too bad (although the near-saintly John is an idiosyncratic exception).
RGB from The Property Of Hate. Painfully blunt and frequently blind to others' emotions, he still protects Hero at every turn.
Zig Zag from Sabrina Online. She may be a slut, but she has been shown to be nice when she wants to. Time will tell on whether the events of Internet/GIFT Arc will shift her character to pure Jerk Ass.
Finn, the protagonist of Sea of Insanity started as a garden variety jerk, but may actually be one of these.
He may be the Alpha and the Omega, the ineffable, the infallible, yes, the creator of the universe himself, but God from Sinfest is placed pretty firmly in this trope. He spends his time mocking and bullying his own creations and the only thing keeping him from being as bad as, or worse than,The Devil is the fact that, well, theDevilistheDevil. Also, that stuff about God being "the ineffable" and "the infallible" and all that jazz I was going on about before? Yeah, thatwasjustbullshit.
Davan from Something Positive, a sarcastic, cynical jerk but nonetheless is capable of great caring and fearsomely loyal to his close friends. In fact, most of the cast are like that.
Charlie from Soul Symphony is pretty rash, condescending, angry, opinionated metalhead. He even talks down to one of his closest friends all the time. We realize over time that he means no harm, and even has a soft spot for those close to him.
Bruno, in Too Much Information: a skirt-chasing jerk, but when he steps over the line and his best friend Ace is going to have to be the bad guy, Bruno announces he has a new job and is leaving. He doesn't. He quit so his best friend wouldn't have to fire him.
Though he is only a jerk to Keidran, we see "Red" from TwoKinds act like one here (spoilers).
Pyramos from Wurr is an arrogant, pompous ass who runs Iacar (the protagonist) and his pack out of hound territory altogether. Why? Because a pregnant female in his pack has lost her mate, and needs a cave for her pups. Of course, there's canonically some question as to whether or not he's got some vested interest in the situation—-which would mean that he'd broken the hound rule against deepblooded mating—but even so.
Jay the Christian fundamentalist in Brüno. In an early arc, when hearing about Bruno's pregnancy, he swoops in to set her straight before she decides to have an abortion. Later he tries again, a little less condescendingly, only to be told that she had already had the abortion. He sputters a bit, then simply asks "...are you OK?"