Ant-Man II, alias Scott Lang. Go after his little girl, Cassie, at your own risk.
The Marvel Universe Ares could, would, and has gone to war with The Heavens Themselves to protect his son, tearing his way through both Olympus and the Japanese heavens to save Alexander.
Nathaniel Christopher Summers aka Cable, after adopting Hope Summers, is this nowadays, and a rather good one too. Hard to believe he used to be an amoral Liefeld character.
Cable's pap Scott Summers too, while not the best dad, he did his best to take care of Nathan (even spending his honeymoon in the future taking care of him because he missed the chance to do so in the present), but he was kinda busy with work. What was his work? Being the leader of the X-Men, that's what.
Reed Richards, along with his Mama Bear wife Sue Storm, of the Fantastic Four, especially given that both their children (Reality Warper Franklin and Child Prodigy Valerie) do have vast powers that make them desirable targets for every supervillain out there.
Norman Osborn learned the hard way to not endanger Luke Cage's girlfriend (now wife) Jessica and their (then unborn) daughter — Luke beat the tar out of him in public, not caring if his already revealed identity took a nosedive in regards to reputation.
During the arc "The Long, Cold Dark," Castle's vengeful nemesis Barracuda targets the Punisher by kidnapping the daughter he unknowingly had with Kathryn O'Brien. When Castle finds out, he is pissed, to say the least, and at one point he spends an hour running electricity from a car battery through Barracuda's genitals just because.
The beginning of the comic, when Barracuda actually gets the drop on Castle and handcuffs him to a chair, then reveals his daughter and holds a knife to her (and trust us on this, Barracuda was going to torture her to death for the sake of revenge). Frank goes into Unstoppable Rage and has to piece together the following events by examining his injuries in a hospital bed. (He snaps his wrist in a heartbeat to get out of the chair, lunges across the room and tears a chunk out of Barracuda's cheek with his teeth. If 'Cuda hadn't thrown him out the window, he would have torn him limb from limb.)
Another Punisher MAX moment. In the story arc "Mother Russia", Castle is charged to rescue a little girl from Russian bad guys (to put it brief: There's a big plot about germ warfare). Upon entering the complex where she is held and meeting her, he says "My name is Frank. If anyone else tries to be mean to you, I will be much, much meaner to them. I promise." Soon after, a skinny, half naked Asian super agent comes and kicks the crap out of Castle with the butt of an AK-47. In a daze, he sees the agent slap the girl. He gets up. The agent throws a kick. Castle grabs his ankle, twists and slams him against the floor, walls, and ceiling until the agent is a pulpy mess and twists his leg off "like a drumstick." Do not fuck with kids around Frank Castle.
Even then, the only reason he stops is because he's scaring the kid.
And yet another MAX moment. Castle is conversing with one of his hooker informants. He's glaring at a pimp, who's guarding over a young girl. He asks the hooker how old the girl is. She says she's about 13 and mentions drugs. Castle walks to the pimp, pulls him into an alley, and emerges from the alley alone.
Punisher: Tell the new guy to behave himself. [walks off] Old hooker: ...that was not my fuckin' fault.
"Kitchen Irish" features a Grandpapa Wolf in Napper French, a retired mob cleaner and the best of his kind. French was legendary for his ability to pull a "Houdini" on a body, to make it disappear completely off the face of the Earth. Irish gangster Maginty kidnaps Napper's grandson to force him to pull one last Houdini...on a live man. He has no choice but to comply, but near the end of the job, Maginty, for his own amusement, shows Napper's grandson what his grandfather had been doing, traumatizing the young child. So Napper decides to give Maginty a firsthand demonstration of how one pulls a Houdini....
The whole reason the Punisher has embarked on his waragainstcrime is one bad day in the park with his wife and kids...
The MAX arc "The Slavers" is another Papa Wolf moment for Frank. Encountering some human traffickers, Castle is so enraged with what these scum do to their victims, that by the end of the arc, he's shocked at what he has done. Including carving up one of the ringleaders, wrapping his intestines around a tree, and then waking the man up.
Osborn himself, though in recent years he's more likely to strap a bomb to his kid and use them as a human shield than he is to protect them, but the original reason he truly came to hate Spider-Man, and why he killed Gwen Stacy, was because he blamed him for his son's second drug overdose, one that nearly killed him.
Peter Parker has his moments in Spider-Girl. Sure, he may be retired and missing a leg, but you shouldn't mess with his kids.
Kaine also shows this trait from time to time when his "niece" is in danger. Must be genetic.
Every incarnation of Peter Parker has this to some extent.... Granted, most versions don't have children, but they all have a big blinking button somewhere in their psyche labeled "someone hurt my loved ones", and the majority of the New York underworld can tell when some idiot has pressed it. Hint: the reason the motor-mouthed superhero hasn't talked in the last sixty seconds is because he's using all his superior intellect and enhanced nerve conduction velocity (i.e. ability to think faster than normal) to consider the merits of the 6,000 different ways he intends to hurt you.
There's also The Amazing Spider-Man (Dan Slott) #645. He's led to believe an infant he was trying to protect is killed. He then proceeds to go on a rampage. It's so bad, that some of his rogues gallery don't believe it...until he comes for them.
Volstagg in The Mighty Thor. Harm, or even threaten, any of his children, biological or adopted, and he will come down on you like the wrath of the angry god he is. IT doesn't need to be his kid either, he'll take you out for harming any child near him.
Howard Stark. Who, for the occasion, had come prepared with a 26-man SWAT team and a team of paramedics, all of which he had (presumably illegally) bribed to do his personal work. "Exactly where is my boy, and how many people do we have to kill to get to him?"
Wolverine, as seen in Ultimate Wolverine. He conceived Jimmy Hudson, and knew of his parenthood, in the middle of an adventure.
In Guardians of the Galaxy, Yondu Udonta is a One-Man Army with his Trick Arrow, leads the ruthless and amoral Ravagers, and is Peter Quill's adoptive father. He survives his M-ship smashing into the ground with little more than a few scratches and then takes down an entire Sakaaran platoon (and a necrocraft) in seconds with the aforementioned arrow. In Vol. 2 he massacres hundreds of his mutinying crew in a matter of minutes and later pulls a Heroic Sacrifice to save Peter from the vacuum of space. Peter mentions that as a kid, he always told the other kids that his dad was David Hasselhoff from Knight Rider, who he thought was cool because he had an awesome car and fought robots. Peter eventually realizes that Yondu fits that description reasonably well.
In Spider-Man: Across the Spider-Verse, Peter B. Parker is now a father to his adorable daughter, and he even made her web shooters of her own.
Western Animation
Ant-Man II from The Avengers: Earth's Mightiest Heroes mainly uses his powers and abilities to ensure the safety and well-being of his young daughter. In the episode in which he officially becomes the new Ant-Man, he punishes Crossfire for kidnapping her by kicking him in the face, then covering him in ants.
