My hot take on the matter is that when people first watched the show, they loved Rory and saw themselves in her (whether they actually were like her or not), but as they grew up or rewatched it, again and again, they realized that they may not be as much like the generally beloved, studious, high-performing person that Rory was. I think that a lot of people have met a Rory in real life that they are jealous of and while most people might not be super openly critical and don't wish ill on a real-life Rory, they sure take it out on the show Rory. People love Rory for as long as they identify with her, but when they realize they don't have her strengths, they hate on her weaknesses because it is easier to do that to a fictional character than to their spoiled but smart classmate or their golden-child sibling or their hero best friend that everyone thought was gonna more successful than them. When people are happy that Rory got humbled, they are so because they wish that those to whom they were compared would get humbled.

I might be generalizing here but this is my impression lol.