The show is about a guy going down the crime route, and Skylar is an obstacle to that. From the viewer perspective, Walter is fun to watch, he's doing something cool. Cooking Meth is cool. But then comes that boring character that nags him about "morality". Boooringgggg, who the hell does this chick thinks she is? I came to watch a show about a guy going in a downward spiral, why is she nagging?
Pardon my "monkey brain" thought process description lol. My point is that from what I've seen, people tend to dislike characters that stand in the way of the protagonist doing the main thing that he's supposed to be doing.
For example, Chichi from Dragon Ball, Goku's wife, tends to be disliked because she "nags" Goku. Her "nagging" tends to be basically reminding him that he's a father and has responsibilities, like helping out at home and financially. It's a shounen so it was always overlooked, but technically Chichi is the only one managing finances, and they've been living off only from her father's wealth. Wealth that eventually starts to run out at the end of the Z series iirc. Goku, for all intents and purposes, is a terrible family man.
But, it's a fighting show. It's about Goku and his friends fighting bad guys. So people don't like when characters detract from that objective, so they hate those characters, even if they are actually being the reasonable ones.