In 101 Dalmatians, Pongo teams up with Perdy to lay the hurt on the two thugs about to kill not only their puppies but all 99 puppies. Their treatment of the bad guys is SCARY. You do not mess with puppies and let their parents find out.
Aladdin and the King of Thieves: Cassim is very protective of his son. While they have been separated for years, he still risks his life and tries everything in his power to keep Aladdin safe.
Although not the biological father, O'Malley from The Aristocats adores Duchess and her three kittens, and he fights quite ferociously to prevent the Big Bad from shipping them to Timbuktu.
Astro Boy: Dr. Tenma in the 2009 film. After he accepts Astro for who he is, it's made clear that he's willing to face the military, its angry Commander in Chief, and its scary indestructible robot to protect his boy. Makes you wonder what would happen if you threatened Astro while there was a chance Dad might get his hands on you.
In the sequels, the titular character of Balto is fiercely protective of his children, notably Aleu in the second film.
Fish from The Boxtrolls. Despite being a shy, cowardly creature, it's evident Eggs is more important to him than anything - and he proves it, too, even lashing out at his attackers when the boy is harmed. He's knocked out almost immediately, but considering the boxtrolls' nature, it was a brave act.
Fergus in Brave is a loving husband and father who would fiercely protect his wife Elinor and their four children from any danger. However, this almost has some serious consequences when he goes after a bear because he thinks the bear has killed Elinor and is now attacking their daughter, Merida. The bear actually is Elinor, who has lost control of her bear form and has lapsed into wild behavior, but Fergus is mad with grief and refuses to listen to Merida's (admittedly crazy-sounding) explanation.
In Coco, when he finds out that Ernesto had murdered him and was directly responsible for denying him the chance to be reunited with his daughter (both in life and death), Héctor was absolutely livid and proceeded to attack the former.
The Croods: It doesn't matter if you're a weird cat/owl hybrid thing, and multicolored sabertooth cat or even a new and more civilized cave person. If you threaten Grug's family, indirectly or not, he will take you down.
Gru takes a level in badass after his three adopted daughters are kidnapped. Among other things, he hopscotches over a group of heat-seeking missiles fired towards him and one-punches a shark!
In a minor case, when the carnival barker denies Agnes the unicorn she wanted, even when she hit the nearly impossible target. He almost makes her cry, and Gru shows him why he should never mess with the adopted children of a supervillain.
Dr. Nefario becomes one in the sequel. When El Macho tries to take over the world with an army of Brainwashed and Crazy Minions, the good doctor, who helped him with the plan, develops an antidote when the villain decides to attack Margo, Edith, and Agnes. A quote after the fact sums up this trope:
Dr. Nefario: I mean, I'm happy with creating an evil army to destroy the world... but nobody messes with my family.
In Epic, Mandrake singlehandedly destroys an entire tree after someone makes light of his son's death. For clarification Mandrake is two inches tall and the tree is around 30 feet.
Marlin in Finding Nemo, because how many fish do you know would risk life and death across an ocean that is infamous for some of the most POISONOUS and DANGEROUSLY VICIOUS creatures of the sea, to find his son? He's not even a shark, he's a clownfish who's scared of everything.
Mumble in Happy Feet Two goes berserk if you try to harm his son. If you are a skua who tries to harm his son, he will bash you aside as if you're a bowling pin. Even if you're an elephant seal, he will RAM YOU!
How to Train Your Dragon: Hiccup is lucky enough to have two of these... one is his biological father, a badass Viking who's willing to punch dragons in the face and dent metal with his hammer to protect his boy, and the other is a freaking dragon. A dragon who attacks and drives off another dragon a little over three times his own size when the other threatens Hiccup.
The Incredibles, Helen and Bob (a.k.a. Mrs and Mr Incredible) do a Mama Bear and Papa Wolf team-up when they take on half of Syndrome's men to get to their kids. When Syndrome kidnaps Jack Jack at the end of the movie, Bob throws a freakin' car at him. The look Bob gives Syndrome when he is told his family is dead sums up this trope. Also, when the Omnidroid tries to crush Violet and Jack multiple times and succeeds in knocking Violet out, Bob gets underneath it Just in Time and supports its weight (which has been estimated by well over 40,780,000 pounds) while telling his children to run, his best Super Strength feat (and probably Power of Love right there). Also the moment when (still thinking his family are dead) Bob nearly strangles Mirage, and threatens to break her in half.
Invader Zim: Enter the Florpus: Professor Membrane may not be all that good at showing that he loves his children, but this movie makes it perfectly clear that he does. Best shown at the climax, when — despite being convinced that everything that's happening is just a hallucination — he proceeds to go all all One-Man Army on Zim's robot army in order to protect Dib.
Whether it's Disney's The Jungle Book or TaleSpin, messing with Mowgli/Kit will get you trouble from Baloo. In the former, he tells the monkeys outright, "Keep your flea pickin' hands offa my cub!" In the latter, discovering that someone has conned Kit leads to a different threat, "Wait until I get through with that guy he'll be able to count his teeth on one finger!" Both Mowgli and Kit even affectionately call him "Papa Bear".
Wolf Boss from Kung Fu Panda 2 seems to have this attitude towards his pack. He absolutely refuses to fire at Po, knowing that his men are going to be killed in the process. He gets killed for all his trouble.
Po's biological father also qualifies, staying behind with several other adult pandas trying to hold off the rampaging Shen and his army while the bulk of the pandas escape. While many are tragically killed, including Po's Mother, Po is ultimately brought to safety in the Valley of Peace and the few pandas that survived eventually repopulate in a safe hidden village, with Po's father leading them.
Sulley from Monsters, Inc.. Harm Boo, and you'll find out why he's the scariest monster on the floor.
Mr. Peabody & Sherman: Mr. Peabody is an almost literal one to Sherman, being a dog and all. He even bites a bigoted social worker trying to take Sherman away.
Spike is a literal example in the Rugrats films. In the first film, he fended off a wolf that threatened the babies. In the crossover film with The Wild Thornberrys, he teamed up with Eliza to find the babies. He even calls them "My babies".
Shrek 2: King Harold might be prejudiced and backstabbing but one thing is certain, he loves his daughter Fiona more than anything else. What finally crosses the line for him is when Fairy Godmother tries to force Harold into giving Fiona a potion to make her fall in love with Prince Charming after realizing Fiona would not be with him on her own free will. Despite her threats, Harold decides at the last moment not to give her the potion.