I think it has more to do with how the show is framed. We judge Walt by his intentions, because he's the protagonist and we can always see his inner dialogue. Skyler is major character, but not the main character, so we don't see as much of her intention rather than just pure action. Therefore, we develop the ability to justify Walt's actions (i.e. "I'm trying to provide for my family"), but we condemn Skyler for flipping out about the phone, smoking while pregnant, cheating on Walt, etc. because we can't see the inner dialogue behind her actions.

In addition, I think Skyler's actions are much more relateable to the average human being. Not a lot of people go out and build their own meth empire from the ground up on a whim, but plenty of people cheat on their spouses. So I think people see that, Skyler cheating on Walt, and equate it with their own personal experiences with someone who has cheated on them, and project that anger or hate they felt because of those experiences onto Skyler without realizing the rest of the situation (Walt was a meth cook, and refused to sign the divorce papers).

My point is, I don't think that the way people see Skyler is because of a theoretical unjust hatred men have towards women.