It's not irrational at all to dislike Skyler, given what we know about Walt's motivation to provide for his family. Lets make clear that Anna Gunn does a fine job playing the character, but it's the character's actions that I dislike. She's continually busted Walt's balls, and then she accused him of killing Hank without letting him explain that he tried to save him. She attacks him with a knife, he defends himself, and gets accused of attacking her. He takes his daughter who he has a legal right to, and gets accused of kidnapping. It could have all been avoided if she went with him and gave him a chance to settle down and explain he was trying to protect the family. And even after all that he ends up calling her and lying about her lack of involvement to protect her from the police, once again taking care of the family given the dire straits he's in.