Timon is an as*hole. People on Lion King forums probably tell you to shut up because you ask questions with such obvious answers. You might as well ask what color Timon is, and you'll probably get the same reaction. Timon's assholitity towards Pumbaa and Simba is just as obvious as the color of his fur. In contrast, since Nala's father is neither Scar nor Mufasa, it must be some other lion. The identity of this lion is unknown within the established movies, and thus is a question worth asking.
So basically, when someone asks why Timon is hated, the common response probably contains a facepalm, whereas when the identity of Nala's father is questioned, the response is probably "I don't know either." The former adds a sort of a social barrier, and the latter does the opposite. It's kinda like a ToM thing. Since people who are different are treated like crap, if you ask a question making it obvious that you're different, it most likely isn't going to go well. Asking who Nala's father is verifies that there are no observable differences in thought processes, as everybody wants to know the answer to that question. When people meet people who are more like them, they are more likely to treat them better.
This isn't just for neurologies, but for everything from common interests, to races, and even species. People don't ever treat everyone fairly, no matter how much they like to pretend they do. This is why people who have a lot in common are friends. This is why people with different beliefs hate each other. This is why animals are sometimes treated worse than even other humans. I can't imagine how we would treat aliens if we came in contact with them. Add in fear to the prejudice, and wow, that's a catalyst for disaster right there.
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Remember, all atrocities begin in a sensible place.