Wow, there are a lot of haters out there:

Because Walter is the show’s protagonist, there is a natural tendency to empathize with and root for him, despite his moral failings. (That viewers can identify with this antihero is also a testament to how deftly his character is written and acted.) As the one character who consistently opposes Walter and calls him on his lies, Skyler is, in a sense, his antagonist. So from the beginning, I was aware that she might not be the show’s most popular character.

But I was unprepared for the vitriolic response she inspired. Thousands of people have “liked” the Facebook page “I Hate Skyler White.” Tens of thousands have “liked” a similar Facebook page with a name that cannot be printed here. When people started telling me about the “hate boards” for Skyler on the Web site for AMC, the network that broadcasts the show, I knew it was probably best not to look, but I wanted to understand what was happening.

Seems targeted specifically to wives:

As an actress, I realize that viewers are entitled to have whatever feelings they want about the characters they watch. But as a human being, I’m concerned that so many people react to Skyler with such venom. Could it be that they can’t stand a woman who won’t suffer silently or “stand by her man”? That they despise her because she won’t back down or give up? Or because she is, in fact, Walter’s equal?

It’s notable that viewers have expressed similar feelings about other complex TV wives — Carmela Soprano of “The Sopranos,” Betty Draper of “Mad Men.” Male characters don’t seem to inspire this kind of public venting and vitriol.

Or specifically targeted to strong women:

But I finally realized that most people’s hatred of Skyler had little to do with me and a lot to do with their own perception of women and wives. Because Skyler didn’t conform to a comfortable ideal of the archetypical female, she had become a kind of Rorschach test for society, a measure of our attitudes toward gender.

Skyler to the haters:

she is a cheater though.  

Yes, and a money launderer and tax evader, too.

And she pays for her DEA brother-in-law's medical bills with drug money.

She has no moral compass. But in that sense she's like almost every other character on the show.

Why is she hated and Jesse Pinkman is beloved? Pinkman is a killer who makes meth.

Is it because Pinkman shows remorse and regret whereas Skyler does not?

She cheated before the cancer...

Remorse may have something to do with it, but I think she was shown to be immoral (cheating) plus all the bad emotions that come with a marriage on the rocks (anger, animosity, etc.) before the cancer situation at hand allowed/lead/forced Walter and Gang down that spiral.