She is hated because she is acting sanely in this situation and is constantly trying to stop Walter's insanity.

Same, and I suspect that not many people ever did hate Skylar... But the narrative makes for good content, so the few that did hate on Skylar got portrayed as the majority.

IIRC, though, Anna Gunn mentioned having a lot of negative interactions with the audience conflating her with her character... So who knows.

She's hated because Walt turned everyone against her - including the viewer, it seems

I like how these conversations always ignore the wrong things Skylar did, such as cheating with Ted. It's always "well Walter was the devil, so anything she did was ok". She still begins the show by showing very little care for his birthday and making it feel like a chore. She's literally part of why he feels he's in a hum drum boring life with no control. His character ark is largely about him going from a meek high school professor afraid to do anything into a completely fearless kingpin who finally has control over his life. Yes, the point is that he goes too far. But it's also shown pretty clearly early on that he feels powerless and like his life is out of control(you know, like a sudden terminal cancer diagnosis might do).

Was Walter a bad person? Yes. Was Skylar also a bad person who didn't truly see him as an equal and who, when given the chance, cheats on him remorselessly? Also yup.

Multiple people can be bad. Even Hank, arguably one of the most moral characters, suffers from major blindspots and is a dismissive dick to Marie.

People defending Skylar are the kind of people that say "I can do what I want because it's a free country" and get shocked when they learn there are consequences to their actions, even if justified.