In Stephen King's The Dark Tower The Good Man, John Farson, while presented to be the bad guy (and actually turns out to be Randal Flagg at one point- and then, in later books, not) is shown to be leading a proletariat rebellion for democracy against the clearly Feudalistic system Roland and the other gunslingers seem to be rooting for. This is partly a side-effect of Farson being The Ghost in the novels, so we don't really learn a whole lot about him. The comic book prequels go out of their way to subvert this and when we finally meet Farson he is power-hungry but happens to be a popular and charismatic leader, and his free and democratic society is really shaping up to be a People's Republic of Tyranny with himself as dictator.
Some folks actually wouldn't have minded seeing Dracula actually beat the main characters. The book goes out of it way to make vampirism seem like the worst thing in the world, but outside the inhuman hunger for blood, receiving the powers of the night and immortality didn't seem like a bad trade-off. Well, at least for themselves; other people might not be so happy with the "being drained of blood" thing. Although the book heavily implies that vampires are essentially corpses possessed by demons that are holding the person's soul hostage, as even Dracula himself smiles when he's finally killed.
There have been a number of works riffing off this to the point of making Dracula the hero, such as Fred Saberhagen's Dracula Tapes.
A lot of fans bash the main characters, and Gryffindor House in general, because of the author's prejudice against Slytherin House, who they view as cultured and urbane in comparison to the crude, bullying Gryffindor jocks. In a slightly different perspective, they recognize most of Slytherin is evil, but criticize the author for making them so, especially considering their defining trait is "ambition", which any normal eleven-year-old would have oodles of ("I wanna be a ninja/astronaut/actor/doctor/lawyer!"). So, to rebel, they generally ignore the fact that Slytherin sucks, and reinterpret them in the fandom to make a more realistic picture of cunning and ambition. In an interview on Mugglenet Rowling defended Slytherin and said "they are literally not all bad [people]". The problem is that they are never shown in the actual books to be anything other than Jerk Asses and Voldemort supporters, which might indicate Rowling has some Rooting For The Empire of her own.
Some people just genuinely wanted the Death Eaters to win the war. Perhaps because they deemed the dark characters to be more interesting, or because the ideology seemed rational, or because they might believe the whole series had an annoyingly Black and White Morality and was a tad too Anvilicious. Or simply because Evil Is Cool.
Dumbledore starts out as Harry's kind, grandfatherly, somewhat kooky mentor, but in the later books, more things about his past and his agenda regarding Harry and the war are revealed, which leaves him more in the Manipulative Bastard category. This has left a lot of fans in the somewhat awkward position of liking Harry just fine and rooting for him, while simultaneously greatly preferring Voldemort over Dumbledore.
The Kingdom becomes The Empire, but are really now The Federation with feudal trappings. The Republic of Haven goes the entire gamut though, from The Empire by any other name to People's Republic of Tyranny under a Reign of Terror to the Restored Republic, giving viewpoint characters to root for and against the entire time. Noticeable in that few civil foes in Manticore get a full viewpoint, while all Haven viewpoint characters, no matter where on the moral line, are given a full viewpoint including motivations. This may have been intentional, as Haven has undergone a slow Heel–Face Turn for some time now. Now that Haven and Manticore have allied against Mesa, Haven are officially the good guys, and rooting for them is expected.
This is also partly due to the authors particular writing style. As a professional military historian he is always careful to portray the tragedy of the war by humanizing both sides, which leads to over all Grey and Gray Morality and sympathetic enemies. When portraying the domestic politics of Manticore, however, he tends to write it as full of straw men for his main character to beat up, causing the Star Kingdom to come off as less sympathetic than the balanced and nuanced Peoples Republic. This only really starts to change around book ten, when readers are introduced to Catherine Montaigne (the first good Liberal we've ever met) and Michael Oversteegen (the first good Conservative we've ever met). From that point on, both parties, which are in opposition to the heroine's Centrist party (and the Crown Loyalists, who are basically de facto Centrists because the Queen is), become much more well-rounded, and the heroine herself is able to recognize and respect the validity of many of their points while still disagreeing with them on certain matters.
The Hatedom has a slight tendency to do this with the Solarian League, partly as a counter-reaction to the League's somewhat inconsistent characterization as either a very loose confederation or a nigh-totalitarian bureaucratic empire, and partly as a result just plain finding Manticore's constant development of new warfare-toys that revolutionizes warfare annoying by that point in the series.
An example occurs in the novel Shadow Of Saganami when the Kingdom of Manticore is in the process of the Empire of Manticore by the (voluntary) annexation of the Talbott Cluster. Local resistance groups are opposed to it, and the most developed are essentially the quasi-libertarian space-cowboys from the subtly-named planet of Montana. The reader is supposed to root for the Empire in this case because resistance, although composed of well-meaning people, aren't aware the people they're resisting are actually the heroes in the setting, and that their resistance is being "assisted" by actual sociopathic terrorists and secretly supported by the Mesan Alignment, neither of whom give a crap about the well-being of the population.
The Hunger Games fandom has no shortage of fans who prefer the Career tributes to Katniss and Peeta, finding them equally sympathetic (or even more so), considering that they have been brainwashed and bred since birth to kill other kids in a horrific child murder reality show.
In the Hush, Hush series, the archangels are written as being extremely unfair, because they threaten to throw Patch into Hell if he pursues a relationship with Nora. The trouble is, Patch is written as an arrogant idiot who spends his days gambling and groping Nora, not showing the slightest inclination to actually do his job. As a result, the archangels come across as trying to get Patch to shoulder some responsibility. Add in the fact that Patch spent almost all of the first book stalking and assaulting Nora and the idea of him facing serious punishment sounds rather nice.
Incredibly common in the Inheritance Cycle. The book concedes that most of the people living in The Empire are happy and at peace, giving the impression that if the Varden would just stop fighting everyone would be fine. And though the emperor is a douche, his evil actions all seem to be about fighting the Varden so, again, his rule would probably be much less tyrannical if the Varden didn't keep going at him. It doesn't help matters that the main character is widely considered to be a Designated Hero with a lot of Kick the Dog moments. Ultimately, the case seems to be more about an Anti-Hero being treated as The Hero, and about the setting's apparent Grey and Gray Morality being treated as Black and White Morality. For every morally questionable deed which the Evil Overlord commits, The Hero commits one in return. The Empire slaughters villages? Well, so does La Résistance, around Feinster. The Big Bad uses conscription? Well, La Résistance whips their own soldiers for doing the right thing, to such an extent that Badass Normal Roran seriously thought that a weaker man would die. The Empire tortures people and uses "true names" to force its soldiers to be loyal to it? Well, La Résistance wields chemical weapons.
Alternate interpretations have the series as a highly biased account given by the real bad guys: the exiled Gondor and Elvish aristocracy, Spartanesque Rohan, and Hobbit mercenaries who destroyed the egalitarian revolutionary Sauron who united the oppressed peoples of Middle-earth. ("Of course, history does not record the savage suppression of the 'Steward's Rebellion' in Ithilien in the early Fourth Age...") The Orcs do resemble those offensive caricatures of trade union workers in early 20th century propaganda... One writer on cracked.com claimed Sauron was actually a good guy who never actually did anything bad in the Trilogy, and that the Orcs joined him willingly due to racism. These ideas ignore the fact at the beginning it is explicitly said Sauron wanted to conquer Middle-Earth brainwashing men into his undead slaves to do so and that the Orcs are clearly enslaved.
Nûmenor. The lightbearer of the Humanity and Civilization, who crushed the Evil Empire of Sauron and broke the fetters of Valar and showed the Eldar where they can shove their immortality. Until Eru cameand spoiled it all. Of course, the Nûmenorans had begun enslaving much of Middle-Earth at this time, which is why so many people hated the Kingdoms created by the refugees.
In The Mortal Instruments, the designated heroes, the Shadowhunters, are descended from the angel Raziel—and pretty damn proud of it. They see themselves as above the very people they're supposed to protect: Downworlders (your werewolves, faeries, vampires, and such) and humans, otherwise known to Shadowhunters as Mundanes (or Mundies, if you want to get really ugly). Honestly, with this sort of Fantastic Racism, you'd probably get more love and respect from a demon disemboweling you and dragging your soul straight to Hell; at least demons are supposed to be cruel. To be fair, the Shadowhunters are called out on this all the time by everyone who isn't a Shadowhunter. The moral of the first 3 books is that the Downworlders aren't inherently evil and the Shadowhunters aren't inherently good and that they could save a lot more lives if they got over their differences and helped each other. Indeed, City of Glass ends with the Downworlders agreeing to help the Shadowhunters defeat Valentine in return for the Downworlders getting representation in the Shadowhunter's council.
Satan from Milton's Paradise Lost, and the biggest reason why Satan Is Good exists in Western media. A case of Misaimed Fandom, as Milton was trying to make Satan a self-centred Jerk Ass with charming but hollow self-justifications for his behaviour, which really stemmed from him being an egotistical bastard too proud to accept how badly he screwed himself over. Part of it is that he never gave any reason that defying the wishes of God is bad, assuming his audience would give Him an Omniscient Morality License. The closest he comes is that He is simply unbeatable so rebellion is a waste of time, even though more angels than not joined the rebels.
Looking at the Star Wars Expanded Universe as a whole, despite the various books that portray the Empire as fundamentally evil, there are also books that show that not all of its members are pure evil, and the Republic/Alliance as not all good (especially with all the Democracy Is Bad, Lawful Stupid and/or Obstructive Bureaucrats going around). Timothy Zahn is the most notable of the authors who do this; Grand Admiral Thrawn, while he is decidedly not a good person, is still portrayed as somewhatbetter than his predecessors (which is not that great an accomplishment), and there are fans who think the galaxy might have been better off with him alive. In the Hand of Thrawn duology, the Supreme Commander was reluctantly seeking peace with the New Republic, and by that point Pellaeon really couldn't be called one of the bad guys. Eventually, he became more or less completely Lawful Good, leading his Imperial Remnant into the Galactic Alliance, the government that succeeded the New Republic after the Yuuzhan Vong killed it. He even became supreme commander of their fleet. Which itself eventually became evil and a copy, more or less, of Palpatine's Empire, though Pellaeon realized this before it was too late, but a bridge fell on him before he could do anything about it (not that he didn't try).
In his Sword of Truth book series, Terry Goodkind tries to avert this by making villains as repulsively evil as possible so that the Designated Heroes' tendency to Shoot the Dog doesn't make the audience turn on him. On the one hand, it means that the villains have all the odious habits that the heroes do, including the self-righteousness, and with extra rape (the only crime the heroes are not at some point guilty of) piled on top, but on the other hand, the heroes are the ones whose Kick the Dog moments we always get to see up close, while the villains' are usually just reported from afar.
The three tracker vampires who are trying to kill Bella, which is seen by some as a sympathetic aim. Each is an Ensemble Darkhorse in their own right.
The books put a lot of emphasis on the Volturi being a power-hungry dictatorship that ruthlessly oppresses the vampire world. The trouble is, the only restriction they apparently put on the vampires is to not be noticed by humans, which is given a reasonable justification (human technology could kill vampires) and very lightly limits the ability for a vampire to kidnap or kill a human. Word of God and the series also show that vampires are more or less animals if left to their own devices, so while their methods may not be lily-white, it makes it difficult to see the Volturi as the dictators the story wants them to be instead of a group of people who are trying to get some sort of order or structure to their world. Meyer tries to make the Volturi corruptness really apparent in Breaking Dawn when it's hammered in that they'll arrive to kill Renesmee and in no way listen to reason... only for them to bring witnesses, reasonably listen to evidence, and leave without killing anyone.
The Seeker in The Host. The Seeker is merely doing their job as the 'front-liner', among the first wave of souls to be implanted into the world's habitants and to smooth the way for more souls to take over, being sometimes forced to use violent ways to achieve this goal, for the sake of keeping the souls save and prospering. The Seeker also took the fact that Wanderer was having difficult subdueing her host Melanie as a potential danger, as a previous incident had happened where a host took control over their body again and severely injured several souls, before the soul inhabiting said body could be rescued and put into another body, the rogue host being disposed of. So the Seeker is quite aware of how dangerous the humans can be, even if they are a small percentage compared to the souls inhabiting the world at the time. Yet Seeker gets repeatedly shunned, insulted and mocked by several characters, the most prominent being Fords and Wanderer/Melanie herself. Given the fact that Wanderer would not have even gotten Melanie's body, had the Seeker not done her job, it not only makes the protagonist seem like an Ungrateful Bastard, but just makes the Seeker more sympathetic to the reader.
The Dark Court of Wicked Lovely, while not completely evil, is far more loved than any of the others.
Happens in-universe, sort of, in a couple of the Discworld books, particularly Lords and Ladies and Carpe Jugulum. In both cases it's really only the witches who are willing and able to oppose the elves (in the first) and the Magpyrs (in the second), and even they occasionally struggle with the temptation; if Esme Weatherwax had a will made of some weaker material (like, say, iron) both books could have ended very differently.