Not every anime character is a hit with the fandom. In fact, many of these hated figures are anime characters who were introduced later on in the series. Characters like Sai from Naruto have a hard time gaining traction because they'll always be compared to the characters who came before them. Meanwhile, other despised characters are there from the very beginning - some, like Haruyuki Arita of Accel World, are even protagonists. There won't be any straight up villains here - instead, the focus will be on characters who viewers are supposed to side with, or at least feel some sympathy for.
This is not to say that everyone hates these characters. Anime fandom is full of such diverse opinions that you could probably find people out there who love Shou Tucker and despise Maes Hughes. Also, a character's presence on this list does not mean that they're objectively bad - only that they have a bad reputation among anime fans.
If you think they deserve the hate, vote them up - but if you think they've been unfairly maligned by the fandom, vote them down.
In a show that's partially about racism, someone is going to have to hold those racist beliefs. While Nina Einstein's hatred of Japanese people serves a narrative purpose, it doesn't exactly endear her to fans. In fact, the Code Geass fandom hates her so much that there are actual discussion groups dedicated to bashing her. Racism isn't all that Nina is guilty of - she also gets heat for her pathological obsession with Princess Euphemia. In fact, she's even shown pleasuring herself on a table to thoughts of Euphemia, earning her meme status. Being in love with a princess wouldn't be so bad if she wasn't willing to end lives in service of her one-sided feelings, but Nina literally builds a bomb because she thinks it will help Euphemia. Yikes.
Ask any random My Hero Academia fan who their least favorite character is, and chances are high that they'll mention Minoru Mineta. The would-be hero is so wildly disliked that MHA fans put up multiple petitions calling for him to be removed from the series. Why all the hate? It seems to be divided into two camps. A lot of people don't appreciate his blatantly lewd behavior. Given how often sexual harassment happens in the real world, it's no surprise that not everyone finds it entertaining in fiction. Some might forgive the perversion if he were sufficiently heroic - after all, a lot of people can overlook this trait in characters from other shows like Jiraiya and Meliodas. But Mineta's powers are far from impressive, and he's cowardly where he's expected to be heroic. Mineta does have his share of fans, but he's far from popular.
Alois Trancy is the protagonist of the second season of Black Butler, but he didn't meet with nearly the level of acclaim that Ciel did. Seen as simultaneously brattier and less interesting than his counterpart Ciel, Alois just wasn't a hit with the fans. His past, which is presented as tragic but is actually a pack of lies, struck some as completely unsympathetic. His over-the-top clinginess toward his demon butler was seen by some as creepy and irritating rather than endearing. If even Black Butler fans can't get behind the over-the-top tragedy and fan service, that's saying something.
Child characters can be difficult to pull off. It's far too easy for them to come across as bratty, spoiled, or annoying, even to viewers who like children. This is especially true when they're one of the few characters their age in the series. For these reasons Chibiusa, the future offspring of Sailor Moon and Tuxedo Mask, grates on the nerves of some Sailor Moon fans. Her behavior might have been easier to deal with if she didn't dominate so much screen time, edging out characters like Sailor Saturn whose arcs are largely ignored.