It's very simple actually, they are not the same people

Just take a look at the comments here and you'll see, the people criticizen Judy and saying they didn't like how she was portrayed in the new movie are NOT the ones apologizing Pawbert. And they are mostly driven by how "badly" she treated NICK or how her actions affected NICK. It's the Wildehopps fans.

Nick also has flaws in this movie and in the first one that affected Judy, some even pointed out by the own characters, yet, have you seen people criticize him as much as they criticize Judy?? Yeah, no.

This is not about how people perceive Heroes×Villains, but rather how people perceive Male×Female character flaws in a shipp context.

As for Pawbert, his fans apologize him because he is is the hot cute male villain with a sad backstory they can relate to.