Firefly from Ace Combat The Equestrian War. There are times when she acts like an a-hole towards other ponies, especially Fluttershy at the beginning (going as far as to smack her!) as well as Derpy and Medley later on. But deep inside, she's just a troubled mare, trying to readjust herself to the circumstances around her. Thankfully, RainbowDash is there to help her.
Brainbent features a few, which isn't surprising since the majority of the cast are dealing with some emotional problem or other, many of them fairly serious. Karkat is probably their reigning champion. He's a shouty little ball of rage and self-loathing, coated in a complete lack of tact, but he is, at heart, a compassionate person. When he isn't buried over his head in his own issues he's genuinely concerned for the people around him, and for all that he can be painfully inept at dealing with his own emotions, sometimes he gives good advice.
Aramus could be argued as in The Legacy Of The Blood Ravens. He's incredibly arrogant, and doesn't hesitate to charge into battle or lead his men into danger, but he'd give his life for the Chapter and in the end, wants what's best for the Blood Ravens as a whole.
Tama in The Lion King Adventures. Despite being the Big Bad of Series Two, she actually saves Simba from dying of a terminal illness in Sick Simba. She changes her ways in Goodbye, Nala, finally becoming an ally.
Shatterstorm and Roaring Yawn both show their jerkish sides when they first appear in My Little Castlevania. However, the moment something traumatic happens, they end up coming to the defense of the ponies they've belittled. In Shatterstorm's case, he's shown to actually be pretty good with kids.
Despite acting like a total jackass most of the time- make that all of the time- Chaos from the Tamers Forever Series still has some moments where he shows that he genuinely respects his other half, and that he can actually be a nice guy when he wants to.
Ryo also fits the bill, or as Takato puts it:
he knew Ryo was just trying to be a friend…a crazy, narcissist, extremely annoying friend, but a friend, after all.
Zao, the Headmaster of the Imperial Naval Academy in The Odyssey. His initial address to the assembled class consists of telling them that they're all going to die horrible deaths in service of the Realm. Despite this, he really does mean well.
L becomes this in Story Of The Century. Or if he'd always had shades of this it makes itself more apparent by the end of the story before he dies. Deconstructed in that his default "Jerkass" behavior pushes people away and he refuses to let on whatever capacity for kindness that he has.
He tries to apologize to Slipstream for belittling her designation as a medic in one episode.
In a rare moment of mutual agreement, Barricade invites Starscream to play video games with him in favor of their mutual hatred toward people.
TD, the protagonist of The Non-Bronyverse can be extremely abrasive, mostly due to his hatred of the fact that he's stuck in Equestria, but he does come to care for those around him, especially the children.