Ron is loathed by many Hermione/anyone other than him shippers (especially those that prefer her with Harry and Draco), with the general complaint amongst them being that they feel Hermione is too good for Ron and could do better than him. And still others are just simply not fans of Belligerent Sexual Tension types of relationships.
Subverted in Paradigm Of Uncertainty: Ron has literally Died For the Ship, but he's not demonized, and turns out to be alive in the third story. The author is on record as saying she regretted killing him off.
Ginny is similarly despised by people who ship Harry with other characters (especially Hermione, Luna, and Draco). She was already a Base-Breaking Character even before they got together in the sixth book, perhaps in response to the Harry/Ginny shippers who were correctly predicting the couple's canonization, but probably more directly related to her increased prominence (and sudden, off-screen character development) in Harry Potter and the Order of the Phoenix. There are also those anti-shippers that feel the relationship was Strangled by the Red String and Ginny's feelings for Harry are nothing more beyond a Celebrity Crush.
Cho Chang also got it bad from everyone who ships Harry with someone else. This started before Book Five, when all we knew about her was that she was a pretty and popular athlete who (gently) turned Harry down on his first attempt to ask her out. It eventually died off after they dated and then broke up.
Although Nymphadora Tonks is well-liked by the majority of the fandom, there's a small but outspoken group of slashers who have a conspiracy theory that she was written into the story at the last minute to prove that Remus Lupin wasn't gay with his friend Sirius Black, a very popular ship. Even though canon states clearly Sirius was much closer with James than Remus. And the fact that Sirius died before they even got together, so her relationship with Remus proves nothing.
There's also another subgroup who were disappointed because they'd hoped that Tonks would be just as gay herself.
Rodolphus Lestrange seems to be disposable for anyone who ships Bellatrix with, well, any other character. This has canon justification: Word of God said Bellatrix loves Voldemort. Hopeless love, as Voldemort's only attraction is power.
Traditionally, Pansy Parkinson has gotten this treatment if Draco is paired with another girl or guy (which is saying something, because she's not exactly treated kindly by canon either). There does seem to be a tendency to avert this among Harry/Draco shippers, though, who simply re-imagine her into being Draco's close friend instead of his girlfriend.
After it was revealed that James Potter was a Jerk Jock in his youth, he suffered this instantaneously overnight in favor of Snape/Lily who refuse to see Snape's (self-acknowledged) faults and screw-ups to insist that James was an evil asshole who somehow forced poor innocent Lily to marry him. Similarly, many Snape fans bash Lily herself for daring to break off her (rather toxic at that rate) friendship with Snape after he called her a "mudblood" (the magical world equivalent of the n-word), blaming her for the incident and insisting that she owed him her love and affection just because he was obsessively in love with her.
The Chronicles of Narnia. Caspian gets his fair share of hate from the incest-shipping large fandom due to the fact that, since his appearance, many fans have started shipping him with either Susan, Peter, Lucy or Edmund. So there's hate from the fans of all the three most popular incest couples (Peter/Susan, Edmund/Lucy and Peter/Edmund) towards Caspian/any of the Pevensie children... even when book canon actually says that Caspian married someone else (Ramandu's daughter).
Amelia Curtis March aka Amy from Little Women is universally hated for "stealing" Theodore "Laurie" Lawrence from her older sister Josephine aka Jo. This hatred can even be seen in films of the book: the writers don't change the ending to Jo/Laurie, but they show Amy in a bad light (removing her extreme tact and elegance in the 1994 version, for instance) and don't include quite nice scenes between her and Laurie (like his rather cute marriage proposal to her) with this same intention. This is especially stupid and/or funny given that Jo rejected Laurie twice, did everything to stop him from proposing — including leaving home — and wanted him to marry one of her sisters (Meg in the first volume, Beth in the second). Jo chose another guy and had a happy marriage (with the bonus that the guy, Professor Fritz Bhaer, was her Big Brother Mentor and beta reader too), but the fandom who still prefers her with Laurie is as strong today as it was over a hundred years ago when the writer revolted... because even BACK THEN the shippers were more worried about who would Jo marry, than Jo's own development as a character.
There is also quite the Double Standard, as Amy is called all kinds of gendered insults and blamed for the whole deal, but the fans conveniently forget that Laurie pushed his feelings on Jo to the point of, as said above, getting himself refused by her twice. So Laurie can do whatever he wants and he doesn't get blamed, but Amy is to be shamed and hated for everything? Meeep.
There's a subset of fans that totally demonise Professor Fritz Bhaer to make Laurie look as a better option. One can understand being uncomfortable with the age difference (Fritz is 15 years older than Jo), but calling Fritz "creepy" and "possessive" and "asshole who talks down to Jo and holds her back from pursuing her dreams" when he's nothing like that... sheeesh.
Les MisÚrables fandom has a contingent out to get Cosette. Granted, it's not easy when your rival is The Woobie. Marius also gets bashed for choosing Cosette over Eponine, because obviously he can't choose who he falls in love with. This is why we can't have nice things.
This fandom is surprisingly violent, and all the crazier since the "choice" is between a girl who survives until curtain and a girl who dies! Also, the book portrays the fan favorite Eponine as a crazed stalker, and the Marius/Cosette relationship is way more supported than in the musical.
The main problem seems to be that, in the musical, Marius knows that Cosette is his True Love (with a capital T) within seconds of glimpsing her in the street. So there's yet another contingent: Marius/nobody, because one girl is a crazed stalker and he's only known the other for ten minutes. The musical also fails to give Cosette any Character Development and makes Eponine much more sympathetic by greatly toning down her stalkerish actions from the book.
Recently there's been a lot of this going on between Enjolras/Grantaire shippers (the majority of the fandom) and Enjolras/Eponine shippers (a pairing that gained a fair amount of popularity during the movie), from both sides.
Marius can also get this from fans who ship Eponine with anyone other than him. One wonders why, as you'd think simply leaving him with Cosette would be much less painful.
Here's a fun drinking game: head to FF.net, flip over to the Twilight Section, and take a shot every time you find a fanfiction in which Bella dies/is made spiteful so a Mary Sue can hook up with Edward. You will die in seven pages.
Approximately half of The Phantom of the Opera fanfics in existence rewrite Raoul as abusive, alcoholic, womanizing, or an indifferent lover in an attempt to justify matching Christine up with the title character — never mind that the Phantom is an emotionally unstable Stalker With a Crush and a known murderer.
Love Never Dies, Andrew Lloyd Webber's sequel to his musical version of the story (which popularized sympathetic takes on the Phantom), actually makes Raoul an alcoholic gambler who emotionally neglects Christine and their son Gustave. Gustave is Christine and the Phantom's child, due to a one-night stand they had the night before the wedding; the whole show builds up to Christine deciding the Phantom is her true love. Needless to say, a lot of fans were not happy seeing Die for Our Shipmaking its wayinto the printed page.
However, the fact that Love Never Dies is responsible for making the Phantom more sympathetic is... arguable. It probably all started back in the Gerard Butler days...
The Dresden Files: Harry/Murphy, Harry/Susan and Harry/Elaine shippers did not like Luccio. Though that became pretty much moot with developments in later books that effectively torpedoed the Harry/Luccio relationship.
God alone knows what will happen if Molly gets together with Harry (Harry seems to have sunk it though). Or worse, Ramirez
Ashfur is generally hated for getting in the way of Brambleclaw/Squirrelflight. On the flipside, Brambleclaw is bashed for getting in the way of Ashfur/Squirrelflight, and Squirrelflight is bashed for the whole Love Triangle thing happening in the first place. And in some people's point of view, Squirrelflight gets bashed for getting in the way of Ashfur/Brambleclaw. A lot of them are mostly joking.
Crowfeather's third mate Nightcloud gets this from people who ship him with Leafpool. Which is funny, because she's just a minor character who has only shown up five times and has only had about five lines of dialogue; she clearly poses no threat to Leafpool and Crowfeather. Crowfeather doesn't even make eye contact with her until Sunrise (and it's not "I love you" eye contact either; it's "Oh, Crap!, she's going to kick my ass when we get home" eye contact). The only reason the rivalry exists is because Crowfeather patrolled her borders to prove his loyalty. In fact, the Erins have even canonically made her possessive, according to Cats Of The Clans, but even then the fangirls aren't happy.
Ever since Fading Echoes, a book that the authors said contained hints at Lionblaze's mate, featured a long scene that basically screamed "Lionblaze/Cinderheart", Cinderheart has been the whipping girl of Lionblaze/Icecloud shippers, Lionblaze/Hazeltail shippers, Lionblaze/Heathertail shippers who didn't jump ship after their break-up, and possibly even some shippers of more obscure pairings. In retrospect, maybe giving the fangirls over two years to make up their own pairings before introducing the canon pair wasn't a good idea after all...
Graystripe's mate Millie is hated for interfering with GrayXSilver, even though Silverstream is dead and has expressed her approval of Millie. Of course, Silverstream gets bashed by GraystripexMillie shippers, but not to the same extent. Also, everyone forgets that Graystripe actually took a fair amount of time to get over his first mate's death, and he even still thinks of her sometimes.
Daisy was hated for interfering with Cloudtail and Brightheart's relationship. Even though absolutely nothing came out of it, and Cloudtail still got back with Brightheart, the hate persists.
Sandstorm often gets bashed for interfering with Firestar and Cinderpelt, despite Cinderpelt being a celibate hero who accepts Firestar's choice.
Ever since SkyClan's Destiny was released, fans of LeafXSharp began hating on Billystorm for being Leafstar's canon mate. The hate was extended to Cherrytail, who got together with Sharpclaw in SkyClan and the Stranger, earning hatred from those same LeafXSharp fans.
After Sign of the Moon, Dovewing started taking heat from people who shipped her sister Ivypool with Bumblestripe, due to Bumblestripe making advances toward Dovewing. After The Forgotten Warrior, the hate reached an inferno when many ThunderClan cats started pushing Dovewing and Bumblestripe together. Of course, Bumblestripe has gotten this due to interfering with Dovewing and Tigerheart. Ivypool also seems to get the hate for interfering with DoveXBumble despite posing no threat to it. Delving into this shipping war will give you a headache.
Older Than Radio: While it may not have an active internet fandom, trope happens to Sir Walter Scott's Ivanhoe, in which the hero marries his Victorious Childhood Friend Rowena rather than Rebecca, who has spent the entire book supporting and pining for him. Two other books, William Makepeace Thackeray's "Rebecca and Rowena" (1850) and Edgar Eager's "Knight's Castle" (1956), attempt to "correct" this ending in favor of an Ivanhoe/Rebecca ship. Interestingly enough, especially given the times in which it was written (when intermarriage was simply unthought of), Scott's fans were so disappointed with his choice, and sent him so many angry letters about it, they forced him to tell them in the preface of a future edition that it would have been impossible for Rebecca to have married Ivanhoe, that it's just a book, and they should really just relax.
The Hunchback of Notre Dame fandom kind of fits this trope. The fandom mostly consists of Frollo/Esmeralda shippers (no matter what adaptation, though most commonly the novel and the Disney version) who are more than happy to get rid of Phoebus to see this impossible ship happen (Obsessed Stalker-Priest who gets deep sexual urges for the beautiful yet Oh So Dumb Gypsy Girl (who is completely pissed at/terrified of said Priest) DOES NOT EQUAL LOVE). However, as improbable as this pairing is, even people who don't ship it are usually more than happy to have Phoebus die in fandomland.
However, this trope applies best to the Disney version, where Esmeralda/Phoebus is actually a canon couple, Phoebus is NOT a complete jerkass and instead falls in love with Esme for real. Yet the Disney fanbase is also rabidly in love with Frollo/Esmeralda - never mind how evil Frollo is in comparison to the original - and loves to write off Disney!Phoebus for the sake of their ship.
There are also those who ship Quasi/Esmeralda because the hero always deservesthe girl, right? Granted one can understand the appeal, since Quasimodo is also made to be much more sympathetic than he was in the book, but still the way shippers talk about Esmeralda makes her sound like a complete and utter harpy who cares nothing for the poor guy's feelings. Apparently holding him up from falling to his death off of the cathedral while Frollo advances with a sword doesn't count for her, nor does saving him from death at the Gypsy court.
Portions of the Temeraire fandom regard Jane Roland as a jaded harpy incapable of love and thus unworthy of Will Laurence. The creepy part is the overlap with the Laurence/Emily (yes, as in Jane's daughter) 'shippers.
Lissa gets bashed by Rose/Christian shippers. In Rose/Christian fanfictions, Lissa sleeps with everybody, is jealous of Rose, and uses compulsion without a second thought, while in canon, Lissa's nice, responsible, not at all jealous of Rose, and feels rather guilty whenever she has to use compulsion. Heck, Lissa gets the same treatment even in some Rose/Dimitri fanfictions since Spirit Bound came out.
Tasha also gets a lot of this. She shows some interest in Dimitri in Frostbite and asks him to be her guardian which he refuses and has been bashed ever since. Despite the fact she's incredibly nice. Though it is kind of justified when you get to the end of Last Sacrifice...
Adrian gets hit by this pretty hard by Rose/Dimitri shippers.
Then there are the Rose/Lissa shippers that have tendencies to demonize Christian and Dimitri (and Adrian to some extent). The amount of Ho Yay Lissa and Rose have canonically does not help.
Let's not even get into the mess that is the spin-off series Bloodlines. Especially after The Golden Lily came out.
Wicked: Fiyero tends to get bashed pretty hard in most Elphaba/Glinda fics, at least those based on the Musical, with characterization ranging from a general philanderer to an outright date rapist. Since his affair with Elphaba was a little more morally grey and got tragically cut short, fics based on the Book tend to be a little more fair. Though, to be fair, most fans of the book tend to look down on Musical Fiyero anyway.
In the second book, we have Candle, who gets a lot of flak from Liir/Trismfangirls (and boys). Only in this case, the hate is not entirely unjustified; Candle actually raped Liir in his sleep and then dumped him with the baby she had afterward.
Some shippers of Hamilton/Sinead do not take kindly to other ships involving either of those characters.
In the Percy Jackson and the Olympians fandom, Rachel Elizabeth Dare is subject to alarmingly intense hatred and bashing from many particularly hostile Percy/Annabeth shippers for having a crush on Percy. The hate only eased up when she became the Oracle's new host and dumped Percy, since being the Oracle means she has to be celibate, sinking the possibility of Percy/Rachel for good.
It also carries over to the Sequel Series, The Heroes of Olympus. Piper and Reyna are unpopular with some Jason/Reyna and Jason/Piper fans, respectively. And after the release of House of Hades, Calypso wasn't well-liked by several Leo/Reyna shippers.
The Hunger Games contains an in-universe example: President Snow threatens to kill Gale if he stands in the way of Katniss' romance with Peeta, whom he has his motives in-universe for making everyone in Panem ship together.
An in-universe example from Aubrey-Maturin. Stephen's wife Diana is killed 'off screen' in a carriage accident. While it initially seems like a way to allow a romance between Stephen and Clarissa Oakes, she ends up being a romantic red herring. A book or two later the real direction is revealed with Clarissa married to another man, and Stephen asks for Christine Wood to marry him.
Poor Aline. She consensually kisses Jace once, while he and Clary are still convinced they're siblings, and promptly decides that he's not her type, is a fairly kind person overall (albeit one with no brain-to-mouth filter), and it's implied that she's trying to figure out if she's a lesbian, or possibly even asexual - yet she is constantly turned into a cruel, backstabbing, relationship-smashing harpy who gets between Clary and Jace, especially in AU fanfics.
The release of City of Lost Souls helped the problem a little - it was confirmed that Aline was lesbian, and none of the characters felt any hatred to her.
Kaelie gets this treatment too even though she only appeared twice and doesn't show any interest in Jace at all. Usually in AU's she gets the same treatment as Aline, in series we know that Faeries don't care much for humans.
In Sherlock Holmes fanfic, Mary Morstan usually doesn't get demonized, but Holmes/Watson shippers will sometimes go out of their way to argue that Watson never really loved her. Which is somewhat eyebrow-raising given that a) Mary dies anyway a few years later, and b) their getting-together was not a casual, easy thing, but went through a fairly tense stage of Twice ShyI Want My Beloved to Be Happy during which Watson desperately and unsuccessfully tried to quash his feelings for her to bring himself peace of mind.
It does occur in a round-about way, though: they often try to argue that Watson was always "neglecting" his wife by going out with Holmes while she was always nagging him to always be sitting at home with her...which isn't once mentioned in canon, and in fact in one story Mary encourages Watson to go help Holmes on a case because she wants him to have some fun! Granted, Mary barely appears in the stories, but still — assuming that Mary was a jealous boring shrew with no evidence to back it up, while ignoring the evidence to contradict it.
Many fans of the Sookie Stackhouse series take this trope to disturbing extremes in their devotion to Eric Northman, one of Sookie's main love interests. Any character is likely become a target if they either behave negatively toward Eric or show a romantic interest in Sookie; Bill Compton gets the worst of it for obviousreasons, but Sookie herself gets a lot of hate for initially rejecting Eric and otherwise not being "good enough" for him. No matter what Eric does, the fans always come up with ways to justify it to a point where even if he outright sexually assaults Sookie in a fanfic, many fans will blame Sookie for it and sympathize with Eric for being driven to such an extreme. Characters who are portrayed sympathetically can be expected to spend a lot of time talking about how great Eric is and encouraging Sookie to concede to Eric's desires, even characters who've had nothing good to say about him in canon. Things came to a head when the last book in the series came out and Sookie ended up with Sam Merlotte after Eric decided to marry another woman for political reasons. Many readers were shocked when Eric demanded that Sookie become his mistress, became angry at her flat refusal, then lamented not having turned her without her consent earlier in their relationship. This really shouldn't have come as such a surprise given the foreshadowing and Eric's intenselypragmaticpersonality, but many fans declared it to be completely out of character and decided to ignore the last book altogether. Indeed, many an epic has been written for the express purpose of providing a "proper" ending to the series, following a long-running tradition wherein fans would write stories after each book to put a positive spin on the latest of Eric's not-so-savoury actions.
Memoirs of a Geisha: Wendy Bateman wrote an entire essay arguing that Sayuri wasn't really happy in her relationship with the Chairman- contradicting Sayuri's own narration- to support Sayuri/Nobu. She goes so far as to attack the author, claiming that Sayuri's fate is a "project[ion] of his own self-hatred."
Essay: Sayuri herself demonstrates her lack of self-respect by choosing an objectively inferior, superstitious man who is her "destiny" (the Chairman) over a strong, kind, virtuous entrepreneur (Nobu).
A Song of Ice and Fire, with its Crapsack World, rarely has characters whom fans kill off merely for a ship's sake (for example, Cersei can die not just for Jaime and Brienne to hook up but also to make space for someone more competent on the throne), but there still are a few straight examples.
Selyse Baratheon who rarely makes it beyond the fifth chapter in Stannis/anyone else fics. Melisandre, Stannis' other canon partner and very hard to kill, can just vanish from the plot if she isn't paired with him.
Sandor Clegane sometimes gets it from the shippers of Sansa/anyone else.
In cases of Sansa/anyone but himself, Tyrion Lannister usually graciously annuls the marriage. However, if the plot is set in the timeline around book three and Sansa is to be paired with Jaime or Tywin (or, on rare occasions, Willas Tyrell), Tyrion very frequently either gets beheaded for Joffrey's murder or just dies randomly.
Brandon Stark is a weird example where this happens to a character that has already literally Died For Our Ship in the text. In canon, he was betrothed to Catelyn, and when he died she was betrothed to Ned in his place, which proved to be a Perfectly Arranged Marriage. However in AU fics where he survives, he's usually portrayed as an at best unfaithful and at worst abusive husband to Cat, usually to justify her cheating on him with Ned. Granted, Brandon is described as being a womaniser in the books, so it's not completely unfounded, but he was also gallant enough to get himself killed trying to rescue his sister and father, so he couldn't have been all bad.