In DnD it's because most undead are damned and tortured souls enslaved by dark magic to the bidding of their twisted masters.

The skellingtons are looking at you, the real you, the core of your very existence with their soul eyeballs. And they hate you, because you are alive, and they aren't just dead, they're being tortured every moment of their existence.

But, hey, tell me more about your perfect medieval civilization built on raising zombie field hands.

/Jokekilling