Skylar's a level-headed, reasonable character that's caught in a completely shitty situation against her will but tries to fit into it to protect her children and family.

Yeah, she's got some flaws, but they don't come close to Walt's issues what with the drug dealing, lying, child endangerment, multiple murders, conspiracy...

People just get mad at Skylar because she (justifiably) gets in the way of Heisenberg-Super-Fun-Time-Drug-Adventures. People wanted Breaking Bad to just be pure escapist fantasy, but that's not what it was trying to be at all, and they blame Skylar for it.