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.
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.
Krosp in Girl Genius. Of course, he's a cat and you have to make allowances.
Another Phil Foglio example would be the Klegdixal ambassador from the Gallimaufry arc of Buck Godot: Zap Gun for Hire.
Possibly also 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.
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.
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".
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.
Netta from DDG usually spends her time thinking up fresh torments for Zip, but can be capable of the occasional sweet gesture.
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 most of the main characters from Errant Story are a bit dickish on the surface but are, at heart, decent people. Jon, Sarine, Sara, and more recently Meji (though that was more the result of maturing as a person rather than revealing something that was already there) all more or less fall into this category. In fact, the only one who is nice on the surface turns out to be a genocidal maniac.
Mora and Rachael from Las Lindas. The writer tries to portray Miles as one, but most consider him just a regular jerk.
Cpt. Dahl from Air Force Blues. At least, when he gets into serious "Danger Zone" mode.
Though his group finds him unpleasant and cranky, Rocky from Our Little Adventure isn't such a bad guy.
Finn, the protagonist of Sea of Insanity started as a garden variety jerk, but may actually be one of these.
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).
Before the S Grub game, Eridan spends most of his time trying to save the very troll castes he wants to wipe out, if only because it would make Feferi unhappy. In Act 5 Act 2, he murders Feferi when she tries to stop his Face Heel Turn... he is probably not going to be an example for long.
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.
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.
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 Jerkass.
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.
Jamie from Khaos Komix is typically depicted as a grouchy, mean, homophobic Jerkass. 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.
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.
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).
Strong Bad from Homestar Runner. He tries to cheat to win contests, bullies around his brother Strong Sad, and left Cloudcuckoolander Homsar for dead, but he does get along well with his co-stars.
Sean "Lucky" O'Cann of Survival of the Fittest acts like a bit of a prick, but has been shown to be genuinely warm and affectionate at other times. It's how he deals with his insecurities, for the most part.
Steg, a popular YoutubePooper, says that although he seems to act quite angry on the Internet, he's pretty nice when you get to know him. And he has a sense of humour.
The Nostalgia Critic. He ridicules old movies and TV shows, shoots characters who get on his nerves, and though enjoyable to watch, definitely isn't a nice guy. When he goes to rip up "Follow That Bird", he spends most of the review squeeing like a Fangirl over all of the characters, finally culminating in this loud declaration:
NC: I CAN'T DO IT! I CAN'T MAKE FUN OF SESAME STREET! IT'S THE FIRST SHOW THAT I EVER SAW! [...] I LOVE YOU ALL! YOU'RE SO BEAUTIFUL AND INNOCENT! YOU ARE CHILDHOOD!
He then proceeds to cry, run away, and pay one of his alter-egos Chester A. Bum to finish the review for him.
And in reality, Doug Walker is nothing like his character. A few people have suggested that because he's so likable and dorkily charming that it rubs off on the Critic and makes him more 'heart of gold'-y than what was intended.
And shall we put his Distaff CounterpartThe Nostalgia Chick up here too? She's condescending, has her moments of being utterly deranged, abuses her best friend and hides all of it behind an overly cute, girly persona. But she nearly always tries to find at least one good point in the crap she reviews, she's smart as hell, she clearly thinks Nella's adorable like the rest of us (just have a look at the ends of her "My Little Pony" and "Ever After" reviews) and, as is with Doug/Critic, Lindsay's likability shines through easily.
Really, aside from the obvious evil characters (Ask That Guy, Sage, Mechie), we could put the majority of That Guy With The Glasses here.
Church from Red vs. Blue is surly, rude, and generally hates everyone around him. On occasion, however, he shown he genuinely cares about his friends, going as far as to utter a Big "NO!" when Caboose - a character with an IQ of -12 who had done nothing but annoy him since they met - when he was killed (he got better). In the season finale of Reconstruction, he sacrifices himself so his friends can escape.
Its more than that, Church could have easily escaped with the rest of the Reds and Caboose, but stayed behind to help Washington, who he seemed to dislike more than anyone because of his freelancer status. Because Church would be destroyed by the EMP, staying behind meant certain death whether or not Wash succeeded. Heroic Sacrifice indeed.
In DC Nation, most of the Outsiders fit this like gloves. Travis is a street kid turned Green Lantern who sometimes forgets there are actual people involved when he starts planning. Green Shield has the Arrow family's moxie with a side order of caustic sarcasm. Caleb and Amelia Zukov love to put up a good show of not giving a shit about their teammates, but God or Hell help you if you if you go after the team...especially if Caleb doesn't particularly like them.
The "Misunderstood D-bag" meme is all about this; describing a behaviour usually associated with douchebags or generally unpleasant people, then giving a reasonable explanation that frequently makes them a good guy.
Kodiak of the Whateley Universe. He chases girls, he pushes people around, he was in the Alphas when Don Sebastiano ran it. But he's been looking for Ms. Right and is sticking with her; he pushes people to see if they'll stand up to him because he has the spirit of the bear giving him superpowers; and as soon as he could kick Don Sebastiano out and fix the Alphas, he did so, even though it meant he could lose his spot as the head Alpha in doing so.
Hashimoto Daichi in Greek Ninja. He's arrogant, selfish and self-centered, and yet somehow... he's not.
Simon, aka Honeydew from the Yogscast. Lewis (Xephos) too, to an extent. They're often seem pushing one another off cliffs, making questionable jokes and burning things For the Lulz but they call each other friend at least once every video, Simon's the first to reassure Peculier when he doubts his abilities as a hero and they often show genuine concern for the NPC's they help out along the way. And then there's their reactions when somebodythey like dies...
