For me, understanding Skyler's role and why she is the way she is is a crucial part of understanding Walt himself. Walt was a man with a certain ambition and as that floundered (because of his pride, likely), they settled into a mundane 9-to-5 existence. Skyler represented in a way that part of his life that reminded him of his failure, of his mediocre life.
What follows for me would be the way it would devolve in a normal relationship. Why wouldn't Skyler constantly hound Walt for lying? Why wouldn't she be furious considering she has a kid with Cerebral Palsy and a new baby on the way? Why wouldn't it shock her that the man who before was a simple chemistry teacher turned out to be cooking meth? Why wouldn't she stand in the way of that at times? How else is she supposed to react?
Anna Gunn's performance is perhaps not the most nuanced, but her character is acting -precisely- how most normal people in that situation would react (right up until the moment she decided to go along with the money laundering). In fact, I was constantly hoping she would find Walt out early on, because of the danger he was putting his families life in.
She fucked Ted because in her position she felt it was one of the few ways she could exercise a sort of power to take advantage of Walt. When we see later in the show how trapped she really is, it's no surprise she handles this the way she does. It wasn't even like it was an affair, at that point things were starting to unravel and frankly Walt deserved it. But even if he didn't, doesn't it make sense from a character perspective that an increasingly desperate individual who found how such a shocking thing would make decisions that seem at times impulsive?
Anyway, this is an open-ended comment, but hating Skyler isn't misogynistic. The REASON some people hate Skyler certainly is, given the debates I got into with people on NeoGAF alone