Animorphs has Cassie. A large part of the fandom thinks she's hypocritical and self-righteous and just can't stand her in general. Plus, in the final book, she's the only character to get a happy ending with the rest of the cast strongly implied to have died in the Bolivian Army Ending.
A Song of Ice and Fire has a number of characters you could call "controversial". That said, some of them are more hated than others:
The most disliked character in the books is Darkstar. Unlike the other controversial characters, it doesn't seem like anybody actually likes the guy. That might have something to do with his appearance being a rare example of Martin breaking the "Show, Don't Tell" rule to make a replacement for Oberyn Martell— he is supposed to be some kind of amazing, witty Badass. Unfortunately, this attempt at an Ensemble Dark Horsewent horribly wrong, as his greatest "onscreen" achievement, a botched attempt to assassinate another fan-favourite— Myrcella Baratheon, an 11-year old girl— only managed to inspire his entire hatedom, based on this appearance in that one chapter.
Catelyn Stark is a very polarizing character, but she remains one of the most unpopular of the main cast for her actions against fan favorites Jon Snow and Tyrion Lannister.
Lysa Arryn isn't particularly popular, either, due to her Genre Blindness, wanting to see Tyrion Lannister executed and indirectly causing the entire plot to kick off. Not to mention she still breastfeeds her six year old son...
Dawn Schafer has gained quite a hatedom in recent years, though most of this can be blamed on her Flanderization from a laid back Granola Girl to a self-righteous extreme Liberal environmentalist. Mallory and Jessi are hated too, fans seeing Mallory as whiny and unsympathetic and Jessi as a badly-written Token.
In the spinoff Babysitter's Little Sister series, Kristy's stepsister Karen Brewer might as well be renamed Dirty Hellspawn.
The Five-Man Band in Black Dogs liberate a girl from the service of an evil magician, and as she tags along with them, she quickly becomes The Scrappy to both the characters in the book and the reader. The nicest character treats her with a polite indifference, and most of the other characters dislike her to some extent because of her uselessness, ignorance of their customs and tendency to fawn sickeningly over the only humanoid male in the party. When she is finally killed she is not mourned by anyone.
In-universe example: In Discworld, the Personal Dis-organizer is an imp-powered PDA that comes equipped with so many malfunctions, warranty loopholes, and annoying personality-flaws, people unfortunate enough to purchase one (or, in Vimes' case, have one foisted off on them by their wives) have been known to snatch up a sledgehammer at the first hint of a "Bingeley-bingeley beep!". The introduction of the Gooseberry in Thud! serves as an in-universe example of Rescued from the Scrappy Heap.
Sam Jones, from the Doctor WhoEighth Doctor Adventures, whose Holier Than Thou and overly politically correct and 'right-on' character was so disliked that her replacement, Compassion, may have been deliberately written as the exact opposite - i.e. rude, snobby, opinionated, and selfish - either to avoid this Hatedom, or to make people say "now that I think about it, Sam wasn't that bad."
There is also a lot of hate for the rest of the Human Crew , as well as Penny, Bug , Taylor , and Astrid. But even they have pretty dedicated, vocal and yes, reasonably sized fanbases. Just less so than others. No one's really the scrappy except Zil...And even he has a few notable followers on Gaiaphage.Com.
Cho Chang draws fans' ire for two main reasons: one, she was Harry's first crush and things didn't work out between them; and two, she was friends with Marietta Edgecombe, who betrayed the DA to Umbridge, and Cho—horror of horrors—didn't turn her back on her friend after that.
Although Cho is more of a Base Breaker for these reasons - along with the above, there are those who feel her arc was necessary to the story and appreciate that she is largely depicted as a Nice Girl despite some hitches in her and Harry's interactions. Then there are those in the opposite camp of the Scrappy theory - they felt that Marietta was a Designated Villain who was the victim of Disproportionate Retribution at the hands of Hermione, and that while Harry had good reason to be angry he'd went too far in feeling her punishment was fully just (and this is at the very best).
A significant portion of the fandom aren't too fond of Ginny Weasley, either. While most of these fans usually point out valid reasons not to like her (such as how she went from a shy little girl to a very bold, sometimes-brash deadpan snarker who was known for her humor and attracted a number of boys without much effort, including Harry Potter himself, over the course of the later half of the books), there are those who hate her only for the fact that she ended up with Harry when they were firm believers in the fact that Hermione was the one for him.
The Last Temptation of Christ features a similar portrayal of Judas as a devoted follower (that is, once JC starts preaching instead of making crosses for the Romans to crucify Jews upon). In fact, during the titular final temptation, it is Judas who appears and reminds JC of his responsibility and the costs if he were to choose another path. It doesn't really help his case that he took money for it; specifically 30 pieces of silver, the standard price of a slave at that time.
Milo Banda is likely the only character in Septimus Heap who is disliked by some fans due to him being constantly away on travels while his daughter Jenna and the Heap family are in trouble and being generally embarrassing for Jenna.
Bella Swan. Many fans, whether they really enjoy the book's content or just see it as So Bad, It's Good, really do not like Bella.
There are also those who hate Edward AND Jacob. While each is the scrappy to the other side, some people are sick of the merchandise fuel despite the ending of the series being determined before the first movie came out.
Renesmee is probably hated by fans and haters more than Bella, Edward, or Jacob combined.
She is also hated because she's more of a thinly-veiled motherhood fantasy than an actual character.
Within the fandom few characters get as much malice as Merrick, a never-before-seen crossover from a different Anne Rice series who somehow became a titular character. Many fans consider her to be the author's personal Mary Sue (evidenced by her impossibly beautiful and talented self showing up out of nowhere and immediately becoming beloved by all other characters, including the previously gay narrator, David) and argue that the entire novel reads like bad fan fiction (people behaving out-of-character, presence of a Mary Sue, ridiculously pointless plot even for Anne Rice...you get the idea). Fans who had managed to survive past Queen of the Damned agreed that this novel was officially the moment the series Jumped the Shark and put all the blame squarely on Merrick's shoulders. Cue dozens of Fan Fics wherein the character is either ignored or killed outright, sometimes to the point of having other characters kill her for being so annoying.
Daniel, the "interviewer" of Interview with a Vampire, has his own hatedom as well. His habit of puppy-dogging behind Armand earned him the nickname "Daniel the Spaniel" from many, many writers.
And after you've done that, pick a character from Warriors. Any character. Now, you can be sure that a decent slice of Warriors fanfic is entirely based around hating that character.
Nobody seems to like Nynaeve either. She is arguably the most obnoxious female character (or character full stop) in the series, which is one hell of an achievement considering what the others are like.
By contrast, Egwene has begun to fall into this role as she does everything from single-handedly re-uniting the Aes Sedai to rediscovering how to manufacture cuendillar. She also manages to drive away, isolate, endanger, horrifically abuse, disrespect, insult, and otherwise screw over all of her friends. By the end of the Gathering Storm, Egwene, by virtue of rallying the defense against the Seanchan attack against the Tower and prior to that, undermining Elaida's misrule has gained a lot of admiration and support in the fandom.