Avatar: The Last Airbender: Some fans root for the Fire Nation out of the opinion they're the best candidate to advance technology and bring 'progress' to the world. These fans also believe that the Avatar himself is a symbol of outdated superstitions and supernatural forces holding back humanity from its true potential, and that the 'Balance' the heroes are fighting to restore is merely the forced stagnation of civilization. As for all the people killed or enslaved by the Fire Nation, and for all the other people they were planning to exterminate along with their native cultures, that's apparently a small price to pay for a one-world government and an industrial revolution. (One thing that can be said in their favour is that the other nations have a large Stay in the Kitchen attitude, while Fire Nation military is open to women and no-one batted an eye at Azula becoming Fire Lord.) In fact, on a character level, many Fire Nation character are sympathetic (Zuko, Iroh, Ty Lee, and Mai) or in Azula's case so good at being bad, earning them massive fandoms. The problem is that all the sympathetic characters turn against the Fire Nation and its goals, for various reasons, and that Azula is revealed to be severely disturbed.
Some fans support the Equalists stripping all benders of their abilities as the only way to put all people on a level playing field and end the oppression of non-benders, even if the benders themselves don't consent to the procedure. Debates on whether or not bending is an intrinsic part of a person and the show's civilization/culture, and if what the Equalists are attempting is a fantastical form of mutilation or not, can get quite heated. The show itself is a bit grey on the issue, showing that some benders can be oppressive but also portraying the process of benders being unwillingly stripped of their powers as analogous to rape. It gets much easier to call them bad guys after episode 6, where they bomb the pro-bending arena and in episode 7 where they attack innocent civilians and kidnap the metal bending police. Complicating matters is that some corrupt benders namely representative Tarrlok feel that rounding up all non-bending individuals, Equalist or not, and imprisoning them, is a perfect way to neutralize the threat.
Many fans comsider Kuvira doing what's best for the Earth Kingdom or being a better leader than the other options.
More specifically, many fans felt that her handling of the Governor in episode 1 was completely in line with a good ruler (i.e. I give your people food and protection if you agree to become a part of my Empire). Also, considering Republic City wanted to insert an incompetent pushover as ultimate ruler of a deeply fractured kingdom, it is hard not to agree with her during the takeover. In fact, it took the entire latter half of the show's Sanity Slippage for many to consider that perhaps, she was not that great of a choice anyway.
More than a few fans wanted Mr. Freeze to save his wife, even when his plans to do so involved killing other people. It doesn't hurt that each appearance made him more sympathetic, with his canonically final appearance in Batman Beyond being one of the biggest Tear Jerkers in the entire DCAU.
Harley Quinn is the poster-girl for Mad Love and an in-universe proponent of Draco in Leather Pants, who honestly believes that "Mr. J" is a sweet guy and the innocent victim of that mean old bat, and frequently helps in his schemes of murder and mayhem. Many fans claim that if given the opportunity, they would do the exact same thing in her position.
The Penguin. The short, fat, fish-slurping guy everyone in Gotham laughs at. It just gives you such a good feeling on those rare occasions when he gets away with his crimes or kicks some serious ass. Or that occasion in that one episode where he told Batman to his face to get lost, because for once it was the Penguin saving the Damsel in Distress.
Ed Edd N' Eddy's titular mainstays. Granted, their schemes are out for making a short change buck and are shoddy and shabbily-built, but considering how Kevin and the rest of the kids are shown and hinted to have long been stuck up jerkasses who thrive on excluding the Eds for simply being "dorks" gets you rooting for them, and celebrating escaping mass levels of Disproportionate Retribution when they can.
An overwhelming amount of Jem And The Holograms fans root for The Misfits. As the theme song says, their songs are better and their antics are very amusing. They tend to deeper characters than The Holograms and without any of the baggage such as Jem's and Kimber's notoriously difficult love lives. It helps that compared to other examples The Misfits aren't really doing anything too wrong. Their misbehavior is rude, sometimes illegal, and they have almost gotten people killed on a few occasions but on default they just want to be the most popular band out there, even if their methods of doing so mean bringing their rivals to their knees.
There were a few Kim Possible fans that at least want Shego to actually beat Kim whenever they have a confrontation, as they find it a bit too much to swallow that Shego keeps being defeated by a teenage spy who shouldn't have been able to take on a superpowered foe hand to hand. Which explains why you have fanfics that say Shego purposely held back in each confrontation they had. For variousreasons.
It isn't uncommon for The Lion Guard fans to root for Janja, Cheezi, Chungu or any of the one shot villains. All the "villains" want to do is eat a decent meal, only to be stopped by the titular Lion Guard whenever they go hunting, because Predators Are Mean. And the guard is hypocritical if you think about it, because Kion is a lion, and thus is a predator.
In Chuck Jones' autobiography Chuck Amuck, he lists ten rules that every Road Runner cartoon had to adhere to, the last of which was "The audience's sympathy must remain with the Coyote." See The Other Wiki for the full list.
Tom, Donald, Sylvester, and Wile E. Coyote from the Tom and Jerry, Sylvester and Tweety, Disney Shorts and Road Runner cartoons respectively, amass a lot of sympathy given their opponents are jerks or Invincible Heroes and reality seems to bend to their will. Tom seems to get the most of it, which is understandable because he's taking abuse from both the mouse who is breaking into his home and often his owners for failing to catch the trespassing mouse, and many episodes make it IMPOSSIBLE to root for Jerry. Jerry sabotaging Tom's attempts to woo a girl cat and ruining his concerto performances, for example, make him downright unlikeable. To compensate in a lot more shorts in the 50s and 60s Tom actually DID win (usually when Jerry acted without provocation).
The retooling of Bugs Bunny. His initial appearances had him as more of a Screwy Squirrel who messed with people because it was fun. The "canon" version only brings the hurt after having been provoked ("Of course you realize, dis' means war!") or deliberately targeted by a predator (The Tasmanian Devil, Wile E. Coyote).
An incredibly popular version of this is the New Lunar Republic - fans who resent the reign of supposed "tyrant"Celestia and would rather Luna take the throne. Whether or not this counts as Rooting For The Empire depends on whether they're rooting for Luna or Nightmare Moon. Luna is not an example because she's ultimately good (if only a little impulsive), and the legitimate arguments against her right to the throne are purely political. Those who flat out rooted for Nightmare Moon... play thistrope straight.
Discord enjoys enormous popularity, many of his fans wanting the fun-loving, Laughably EvilTrickster to succeed in his goal of eternal chaos. It didn't hurt that in his introductory episode, one of the main characters (namely Pinkie Pie) seemed perfectly fine with a guy who makes chocolate milk rain from the sky. To some extent those fans got to have their cake and eat it too when Discord was freed and reformed without losing his wacky personality.
The Changelings have their fans, arguing that despite the cruelty of their queen, most Changelings just want somethingto eat. The writers seem to have picked up on this, and the Changelings have had a HeelRace Turn — except for Queen Chrysalis.
Given his HORRIBLE childhood, it's not hard for Phineas and Ferb fans to want Doofenshmirtz to win just once. It helps that most of his plans are pretty harmless. This actually happened a few times, with Perry learning the plan and just letting him do it when he realized it was either harmless or something so petty that it might as well be.
Played with X9 in Samurai Jack. The episode he is in focuses on him, showing that he was hunting Jack because Aku was holding the robot's dog hostage. The episode was designed for you to root for the poor robot. Jack cuts him down without a pause; he's just another robot mook to him.
Also while Bart is presented as a Big Brother Bully many episodes show Lisa giving just as good as she gets giving her even more of an advantage since when ever they have a physical altercation she will win and her retaliations are usually Disproportionate Retribution. In the end while Bart should still be held accountable for things like destroying Lisas centerpiece, her career as a babysitter, etc. It is still easier to root for him over Lisa.
One-shot character Hank Scorpio is a Bond-style super villain, but he's such a Affably EvilBenevolent Boss that he's genuinely likeable, to the point that him taking over the east coast in the end is considered a Moment of Awesome.
In episodes made after the movie (and some before), Mr. Krabs' schoolyard-bully gloating of Plankton's failure makes Plankton the more sympathetic character to the audience. What doesn't help is that the mass flanderization of both characters has led Krabs to have fewer redeeming aspects than Plankton. In some cases, Krabs actually goes out of his way to ruin Plankton's rare legitimate efforts or make him miserable in the same ruthless manner as vice versa, and due to their roles, is more likely to succeed (eg. "Plankton's Regular").
Can happen to Spongebob himself, especially in episodes where he goes up against Squidward. He may be a Jerkass, but Squidward is also the show's Only Sane Man, The Chew Toy, Butt-Monkey, andDeadpan Snarker, so he gets sympathy from a lot of fans compared to the obnoxious, inane, callous, and occasionally sociopathic title character. It's different in episodes where Squidward picks on or tricks Spongebob, but often his motivation is just to avoid him and be left alone. Imagine if you had a neighbor like Spongebob, and this becomes a rather understandable desire.
Star Wars: The Clone Wars in general already had this given the Evil Is Cool nature of a number of the villains as the show improved, particularly the regular battle droid, who mostly come off as Punch Clock Villains doing what they're ordered to, never appear especially malevolent, at times descend into Ineffectual Sympathetic Villain territory due to how hilarious they are. But in an interesting case of Evil vs. Evil in the episode "Massacre", this trope can still be applied with outnumbered Asaaj and the Nightsisters taking a much larger droid army led by General Grievous. Grievous, unlike Assaj, has no sympathetic qualities to him, but many viewers were rooting for him and the droids due to Asaaj and the Nightsisters earlier actions during the Nightsister trilogy of episodes, and that he had the battle droids, who came off as more likable than the Nightsisters.
Star Wars Rebels was less prone to this its first two seasons beyond the same general Rooting for the Empire from the movies, as being a kids' show the villains were often either less evil or cartoonishly flat. And then Season Three imports Canon Immigrant Grand Admiral Thrawn from the Legends timeline....
Many Titan Maximum fans want Gibbs to destroy the insufferable main characters. The show was left in limbo with a cliffhanger of Mercury being incinerated by the sun and the heroes have no ship to fly off... so he already has.
A large part of the Total Drama Presents: The Ridonculous Race fanbase started backing the Ice Dancers if only because they're so entertaining to watch and did display considerable skill even before they turned full on villain. Many fans wanted them to win and were not pleased when they didn't even make it to the final two.
A small contingent of Transformers fans feel that the Decepticons are the real good guys, and that the Autobots are evil. Granted, a few continuities show that the Bots aren't perfect paragons of justice, and the Cons had good reasons to rebel, but stories where Decepticons take small children hostage (or killa puppy) show that they are NOT nice mechs.
Given a bit more weight in Transformers Animated in which the Autobots are the ruling empire led by someone who's just a bit too willing to do bad things to achieve victory for comfort while the Decepticons are the scrappy rebels, albeit vicious and ruthless ones.
In the IDW comics the Autobot government was evil (well corrupt at least) and the Decepticons were laid off blue collar workers living in slums until this one miner showed up... (Most of the story is set millions of years later, by which point they're rather less sympathetic.)
One of the movie prequel comics showed one part of the falling out between the Autobots and Decepticons was Prime wouldn't allow Megatron to attack a hostile force on their way to Cybertron, until they arrived and started attacking. Megatron was just trying to protect Cybertron.
In the Transformers: War for Cybertron continuity, Megatron was initially a gladiator who rebelled against an oppressive, caste-based society ruled by the Autobots, so initially it was the Autobots themselves who were the Empire and you should have rooted against. But Megatron became too prideful and ruthless, to the point his ideal of a caste-less society was buried by his desire to rule. Transformers seems to have been moving over the years from "Decepticons evil, Autobots good" to an almost Star Wars-like setup, where Cybertronian society badly needed shaking up but the Cons went too far and the necessities of war turned the Autobots into the casteless society the Decepticons wanted, while the Decepticons became too obsessed to remember their original intentions.
Transformers Prime depicts the Decepticons as having a colorful range of personalities. For some of the less evil ones like Dreadwing and Predaking, it can be hard to not root for them at times.
Recent series and the movie franchise have picked up on some of this and have begun portraying Optimus less like a Christ-figure and more of a President Lincoln: He is still the big good and leader, but the war has taken the toll. He still believes in his convictions that Freedom is the Right of all Sentient Beings, but is weighted by the high cost, loss of life, corruption of allies, and weariness of the millions of years of war. Optimus is still the Big Good of any setting, but he's not blind to the fact that the Autobots are not all virtuous and the Decepticons aren't all villainous.
Many fans and detractors of Ultimate Spider-Man find themselves cheering on the villains. Drake Bell's Spider-Man is a real Base-Breaking Character and his teammates are MASSIVE Jerkasses who bully and mistreat him constantly, all of which make the protagonists look Unintentionally Unsympathetic. The villains on the other hand are Creepy Awesome characters channeling Evil Is Cool and tend to be the part many people think is worth watching. There's also the fact that some major villains on the show are portrayed in a very sympathetic light. Particularly Venom, who is actually Harry Osborn, who is genuinely a good person, who cannot control the symbiote and is easily the most sympathetic character on the show. It really doesn't help that these villains are voice by beloved veterans like Maurice LaMarche, Clancy Brown, and Tom Kenny.
In The Venture Bros. Daddy Venture commonly forgets about everyone and everything important to him. Anything halfway decent he horribly abuses. The villain, the Monarch, cares about his named henchmen, cares about the emotional health of his prisoners and participates in the 'Scared Straight' program when he spent time in the slammer. If it wasn't for the Monarch's occasional efforts to outright rip apart the Ventures, it'd be hard to tell who was the villain. Many viewers will compensate by rooting for Brock, who's a friendly, cool guy that genuinely cares about the Venture boys as if they were his own sons, and yet over the course of the series racks up a higher body count than Dr. Venture and the Monarch combined. Lampshaded at one point when Dr. Venture is groomed to be a villain, and shown to be a better potential villain than heroic Super Scientist.
X-Men: Evolution: The original Brotherhood members just don't come off as evil to many fans, despite all the horrendous things they did. That they are just the "Bad" in a The Good, the Bad, and the Evil situation lends a certain degree of sympathy, as does how they're constantly abandoned or generally treated horribly by everyone, including their supposed allies.
Avatar: The Last Airbender: In "Ember Island Players", the eponymous theater troupe put on a play based on the Gaang's adventures in the series (wildly innacurate and badly flanderized). But this being a Fire Nation troupe, performing for a Fire Nation audience, ends with Ozai using the powers of Sozin's Comet to kill Aang and Take Over the World. To the audience this is the Happy Ending. The Gaang are...less than thrilled.
In Garfield and Friends Garfield tries to tell the story of Hansel and Gretel to Nermal, but Nermal ended up feeling bad for the witch at the end of the story, forcing Garfield to try and come up with an ending that gives the witch a much happier ending. It should be noted that Nermal's horrified reaction to the story didn't really stem from him being evil by any stretch of the means, but rather his innocent persona prevented him from really seeing the witch as evil.
In the Rugrats "Passover" episode, Angelica immediately identifies with Pharaoh and feels sorry that she loses.
In the Family Guy episode "Herpe the Love Sore", Peter and his friends get beaten up by a group of bullies, who are allowed to get away with it because they're American soldiers. Afterwards, an exasperated Peter says "I can't believe I have to root for Afghanistan now."
In a re-packed version of "Mickey and the Beanstalk" which was originally featured in Fun and Fancy Free in which Ludwig Von Drake tells the story to a beetle named Herman, after Willie the giant falls to his death Herman starts crying, when Ludwig asks what was wrong pointing out that everything turned out alright for the heroes, Herman states that he liked Willie, Ludwig assures him that it never actually happened and it was a work of fiction, only for Willie himself to show up alive and well.