People don't like Catelyn because they get the impression that virtually nothing would have shaken her from her own point of view, barring unmitigated circumstances. She would have taken pretty much anything as something which reinforced her initial position, rather than the other way around.
If Ned had told her the truth about Jon, she would have doubled down on her position about him being a threat, and worse, she would have considered Ned a threat to her child (the heir of his seat) for making a "rash and dangerous judgement against the better interests of the family" I.E her child.
Catelyn later on at least loved Ned enough that I doubt she would have betrayed him, but given the first opportunity I totally see her exiling Jon the moment Ned wasn't around.
Which is really the one point which makes her better than Cersei, if not altogether likable. She probably wouldn't have murdered Jon, if only because she knows it would make her children hate her. Cersei pleads the fact that she loves nothing more than her children, but mostly as extensions of herself and how they reflect on her.
Catelyn and Cersei are only superficially similar. One's love is always recursive and self-interested, and the other's is more selfless and implicit.
Both make irrational judgement calls they shouldn't.
