"Geez. That Lizard Folk is a jackass, but he doesn't deserve this. It's like watching someone duel their own puppy."
Tsukiko has no patience for living beings, only the Undead, and positively bullies Redcloak. But the Monster in the Dark knows that at least half the reason for this is that she's always been treated badly by the living, and she can trust the Undead. As he comments after Redcloak has her killed and eaten by her "children" Tsukiko just wants to be loved.
Drowtales seems to like this one, half the cast seems to suffer symptoms of this. Perhaps most notably:
Her mother, the Val'Sharess Diva'ratrika, is, by most counts, not an especially nice person, but very few people think that she deserved to be betrayed by three of her own daughters and left to die in her throne room.
Given that this is a Crapsack World where even small children are expected to know how to fight to death if need be...
Jamie in Khaos Komix is homophobic, a bully, and just all around mean. It's hinted at in some of the earlier stories, but it's not until his chapter (the last one) that the reader finds out that he was sexually abused by a neighbor when he was a child and physically and emotionally abused by his mother. He doesn't think of this as a Freudian Excuse, though, insisting in his internal narration that he's just a jerk.
Candy from Girls with Slingshots: a petty, nasty little (un)professional dominatrix, who was (is?) the closest thing the strip had to a villain...until Jameson (her best and only friend) tells her off due to the increasingly mean pranks she was playing on Jameson's fiancée, Maureen (up to and including replacing their wedding rings with baby seal leather cock ringsat the ceremony). You can't help but feel sorry for her when Jameson tells her to go pound sand. And doubly so when guest star Davan - possibly the king of this trope among webcomic characters - calmly but brutallylampshades her stupidity.
String Theory has Dr. Schtein, who is an absolute Jerkass. The revelation that his mother abused him, his emotional failings, and the fact that he spends the majority of chapters 2 and 3 either ill or beaten up launch him into Jerkass Woobie territory.
Zimmy, who viciously lashes out at random people. But then, she's constantly under strain, never sleeps, and stuck with an uncontrollable ability she expects to last until she dies. And there are two other students she cares about.
Recently, Ysengrin, of all forest people, was moved close to it.
Fan: God, I just want to pet the poor murderous bastard. It's nice to see him evoke an emotion other than fear or anger.
Jeanne. She's separated from her lover and turned into a human sacrifice by her friends, meets her lover again only for him to be murdered right in front of her, lies at the bottom of a river alone until she dies, and is forced to guard the river as a ghost until her soul rots away. Her reaction to seeing a genuinely happy teenage girl is to assume she's mocking her and try to kill her.
Luka of The Meek is a vengeful badass dictator who comes from an extremely misogynistic and warlike culture and has a tumultuous relationship with his wife and children. At the same time, his life has been one long string of Break the Cutie that's left him physically mutilated, and despite the above, he does seem to genuinely love his family.
And unfortunately, as if to prove that things really CAN get worse, his beloved wife dies a horrific death right before his eyes. This not only sent his Woobie points through the roof, but also seems to have final broke him, and he seems well on the way to taking the step to being a Woobie, Destroyer of Worlds.
Then he sees an alternate universe version of his mentor destroy Prospit right after he finally wakes up, watches his team fall apart, eventually culminating in Eridan killing two of Karkat's friends and blinding another, and the nicest troll of them all goes insane and decides to kill everybody. The poor guy really needs to be cut a break. (His comments about certain elements of troll romance make it clear that he thinks no one will ever be able to hate him as much as he hates himself.)
Gwynn in Sluggy Freelance. She's ill-tempered, humorously violently abusive, petty, and selfish, and usually has a kind of love-hate relationship with even those who are the closest to her. But as time passes, we also get to see her uncertainties, weak moments, and regrets over being so selfish as well as so aggressive towards others when she was really being defensive because she knew she was in the wrong. She has some really rough times, too, as the story goes on; there was a time when she may have had it harder than the other characters, though by now, almost everyone's gone through enough hell to surpass even that.
When we first meet Kieth from TwoKinds, he is kind of a jerk to everybody. The 'Hero' is justified, since he has a reputation for being evil, but Flora seems to be a target of Fantastic Racism. Turns out he Was bullied and looked down on by his father for being weak. Was framed for killing his mother and father when he was a child, which had him exiled from his homeland. After that, he met up with the Catfolk, fell in love with one of them, only to be stood up on his wedding day. All of this is revealed to the audience and resolved in the course of two days. Suddenly, his Jerkass behavior seems a lot less mean spirited then it did three hundred comics ago. Did we mention that in those two days he had to watch two people he cared about die (one of whom he killed), and tried to kill his new love interest? Guy has had a really bad day.
Black from Grey is... definitely fits the bill—however, the comic plays its cards very close to the chest in the beginning, so before readers know anything about him, he just looks like a Jerkass.