Only if you perceive it as such. Vince Gilligan sees Skylar as a good character: she stands up against her husband, right? Odd that you think he's a misogynist.
I do think it's unfair that Skylar receives all the hate when her husband is way worse; but that's down to the viewers, not the actual writing itself.
Also, a "good" character isn't necessarily a character that's perfect in your eyes. Many didn't like Lydia, but she was a good character - she had flaws, complex motivations, and played an important part in the storyline. Watch her expressions when she talks to other characters. She's a nervous wreck - not some sort of "you go girl!" strong womyn caricature.
Enjoy it for what it is. It's in no way misogynistic; It just suffers from (mostly) unlikable female characters. And that's OK. People are people, I can connect to them no matter their gender.