Nah this is why.

tldr: everybody hates fat chicks.

That and she fucked Ted.

/s

In all seriousness, in my opinion, she's the most human character on the show. She's an emotional mess that tries (and fails) repeatedly, never giving up. She makes hasty decisions, she has poor judgement, she's quick to anger, and she lacks objectivity.

People see themselves in her, and that scares them. Skylar is afraid of making the wrong decision and never strays outside of her comfort zone, whereas Walter is always taking big risks and trying to move forward regardless of the cost.

It's not that she's a buzzkill, but why she's a buzzkill -- she has some redeeming qualities and makes a few good decisions, but overall she's very easy to dislike. We can see her decision making thought process, and we are shown, step by excruciating step, how much damage she does. Watching her is like watching a car crash in slow motion.

Some of the things she's done are controversial but they end up being the right thing, but generally we're shown non-stop fuck-ups again and again.

If we saw Walter fail as much as Skylar does then nobody would watch the show, but instead we're overwhelmingly shown his victories. That contrast alone influences people's attitudes towards her very strongly, if not more than anything else.