Ron and Ginny Weasley of Harry Potter are loathed by many militant Harry/Hermione and Harry/Luna (hell, pretty much Harry/anyone not Ginny) shippers, and have been since the author confirmed Harry/Ginny and Ron/Hermione as canon in Harry Potter and the Half-Blood Prince. Ginny was hated even before then, 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 in Harry Potter and the Order of the Phoenix. There is a (much) smaller subset of shippers who bash Harry for being "stupid" enough to choose Ginny over Hermione, or who would have preferred to see Ginny get together with Harry's rival Draco Malfoy.
Militant Harry/Hermione shippers (or "Harmonians" to differentiate from non-militant H/Hr shippers) have become so notorious for their utter demonization of any character who gets in the way of their ship that militant shippers in any other fandom will sometimes be called the Harmonians of the fandom.
As noted on the Ron the Death Eater page, the Weasleys in general tend to get this from rabid shippers. Ron and Ginny get killed off in rather graphic fashion in fic, often before the story even starts, or have their faults (real but minor or invented from whole cloth) blown to ridiculous proportions.
Cho Chang also got it from almost 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. This extended into real life when actress Katie Leung was picked to play Cho in the films. She got criticism of her looks and her racial background, and even got death threats.
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.
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.
Subverted in Paradigm Of Uncertainty: Ron has literally Died For Our Ship, but he's not demonised and turns out to be alive in the third story - the author is on record as saying she regretted killing him off.
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 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.
Les Misérables 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.
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.
I think seven pages is giving a little too much credit...
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 way into the printed page.
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.
The Warrior Cats fandom has quite a bit of this: Ashfur is generally hated for getting in the way of Brambleclaw/Squirrelflight, and Spottedleaf and Sandstorm are bashed for loving Firestar.
And 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.
Nightcloud. 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.
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...
Millie.
Of course, Silverstream gets bashed by GraystripexMillie shippers, but not to the same extent.
And they all forget 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.
While it may not have an active internet fandom, a classic example (Older Than Radio, even) for this trope is from 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" and Edgar Eager's "Knight's Castle," 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 and Phoebus isn't a complete jerkass and instead falls in love with Esme for realz. 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 heroalways 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.
In the Vampire Academy fandom, 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.
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.
