Yes, most people dislike Catelyn for her hatred toward Jon. I can't disagree with them, Catelyn was awful to Jon. (Though Jon must keep in mind that he had ten times the life of any bastard could dream of even with Catelyn sniffing and grimacing at his heels) I share your antipathy anyways, only the reason is not Jon.
First off, she has a terrible judgment and somehow never comes to realize this. There's this business capturing Tyrion, but let's leave that be, she was overcome and blinded with maternal instinct. But after Tyrion was gone and she reunited with Robb and saw him safely to Riverrun to the Blackfish and Edmure. She visited his father on his deathbed, very nice and admirable of her, but why not return to Winterfell? Even when Robb wanted her gone she lingered. And THAT is why Bran and Rickon were 'murdered'. Catelyn kept going on in ALL her chapters about how she suffered from having left her children behind. Well she had tons of chances to go back to them and she never did. That's why I couldn't exactly feel sorry for her when she got the news of Bran and Rickon. Second, she was absolutely convinced that no one knows things better than her and no one is a better mother/wife/woman than her. We come back to Tyrion once again, trusting Littlefinger, abandoning Bran and Rickon, telling off Edmure all the time, telling Robb what to do. (Though it's true the Queen of Throns had it right, kings should listen to their mothers, Catelyn DID see Theon should not be reunited with the Greyjoys) And if I recall well, it was Catelyn who suggested to give half Robb's forces to Roose Bolton. As for the other part of this second reason, I was simply going mad every time Catelyn judged a woman by the size of her hips. Jeyne Westerling was of course an awful choice (she was right, thinking of the Red Wedding) and had an ordinary face, but at least she had good hips. That Frey girl, Roslin, oh the poor creature she has such little breasts and narrow hips, poor Edmure how'll she bear children... I'm not a feminist, nowhere near, rather the contrary, but it was always Cersei's line coming to my mind when Catelyn commented someone's hips. "I'm not a brood horse" she said. Well I found it quite an ill thing that Catelyn looked at the young brides like brood horses for sale, counting their teeth. Of course, she herself is perfect, had 5 children thanks to her perfect hips and breasts and didn't even grew ugly as Lysa.
Thrid, her flirts with Littlefinger as a girl. That was unfair with him and with Lysa too.

You are right in your assessment of the late undead Lady Stark. She pushed those five strong pups out like a champ all while adjusting to the rigors of the north. But Cat was always the pretty one so we are told, one just tends to overlook it in her because she is so unattractive inwardly. As much as I dislike the female she had a few graces. She loved her children, though she was stupid in how she saw after them. I never would have allowed Arya to go to court. It ws not as though she and Sansa were close, spending all their daylight hours together. She had ( Jayne?) and needle point, and all the pomp of the royals. I agree that a lot of what happened lay at her feet. All those things aside I would have played The Queen Of Hearts concerning that bitch...you know "off with her head!", just for the way she treated Jon. I can understand her pain at having him as a reminder of Ned's so called infidelity, but to open dispise him...no. Then when Bran fell she had the stones to tell my Jon, ''it should have been you." Still in all, you know as much as I dislike this Stoneheart whore I hope she is around long enough to know the truth about Jon.