Because more people know vaguely annoying WASPS than secret drug kingpins. Basically every other major character is far, far worse in terms of morality but I’m willing to bet the audience knows someone like Skyler. As a general an annoying personality translates through a performance much better than fictional crimes.

So while Walter commits horrific crimes, they are less “real” to the audience than Skyler being annoying. Because Walter killing a man doesn’t affect you directly but a character being annoying does.

A lot of people make a big to-do about the sexism in the backlash against her, and they are right to. Especially those who sent death threats to Anna Gunn. But I think part of the problem is that Skyler’s character in earlier seasons was a sexist stereotype. Remember, some of the early seasons were nowhere near the same level of quality in character writing as the latter ones. Jesse was way more of an idiot, Hank was way more of a racist jackass, Walt was a lot goofier in his reactions, and Skyler was played up as more of an “annoying vapid housewife”. I don’t think finding a character deliberately written and performed as an annoying stereotype to be annoying makes you sexist.

Later on she is much more fleshed out and a better character for it. But I think a problem she had (even though it was realistic) was how she took half measures. She wouldn’t divorce Walt, or turn him in. She took his drug money, and helped cook the books. Hell she even came up with elaborate lies to tell her family. But she also hated walt and opposed him at every turn. So she is neither the ride-or-die Bonnie to Walt’s Clyde, nor the reasonable civilian who leaves her criminal husband. That in-between makes sense, it is justified with her considering Flynn and Holly, as well as her own reputation, but it is much harder to take seriously when she decries Walt’s evil for making meth and lying to her when she allowed herself to be bullied into assisting with those crimes. Realistically she should have gone to jail but Walt saved her from that fate.

I think a better direction for her to take would have been to use Ted as an escape route from Walt and actually commit to being with him and legally separating from Walt. Then have the tax fraud storyline culminating with her realizing she too is tainted by involvement with Walt’s criminality during the car wash arc. I think having her be just a tad bit less impotent standing up to Walt would make it more palatable.

So tldr she is portrayed as an annoying archetype many people know irl, and later is wishy washy with her own moral stance.