But that was exactly my point. Casting Animate Dead is an Evil act. But
why is it an Evil act? Because it has the [Evil] descriptor. But why does it have the [Evil] descriptor? Because some designer somewhere was under the impression that all Skeletons and Zombies are inherently evil, and so creating one would be physically unleashing Evil into the world. This begs the question, "why are Skeletons and Zombies inherently evil?" And if the answer is "Because they run on negative energy," then you have some serious thinking to do with regards to the nature of negative energy. If you decide that negative energy is
not inherently evil, and can't come up with some
other reason for why Skeletons and Zombies (and other
mindless undead) are inherently evil, then the only logical conclusion is that they aren't, and the designers were mistaken when they put "always neutral evil" in the Alignment entry. You should then drop the [Evil] descriptor from Animate Dead (though not necessarily from Create (Greater) Undead), because if negative energy is Neutral and Skeletons are Neutral then there is no reason that making one should be Evil.
Back to the original topic, I think it has to do with psychology. Zombies and Skeletons represent the
other. Something that physically resembles humans, but cannot be communicated with, and has a psychology so alien that we cannot predict their thinking. But the most terrifying part is that
you could end up like that. They are a force that cannot be controlled, reasoned with, or even understood.
Unfortunately, that's nothing like how the undead are represented in D&D. With a few exceptions, undead do not self-propogate. There is relatively little chance of you turning into one, which is one of the biggest things that make undead so terrifying (in my opinion, anyway). And even if your character does turn into a Wight,
you, the player, do not. You just say "crap, guess I have to roll a new character" and get on with the game.
As the DM, you can choose to implement some of the psychological reasons for hating Undead in the NPCs you make. Maybe, even though in your world Skellies are Neutral, the NPCs are unfairly prejudiced against them because of the reasons above. Or, if you think Skellies
are Evil, maybe the NPCs are totally justified in their hatred, because uncontrolled Skeletons keep wandering too close to town and killing the livestock.
In the end, it's important to take away a certain lesson from this. Even in a universe with Objective Morality, it's important to think critically about
why certain acts are Good or Evil. If all you can come up with is "Because the book says so", even when there's plenty of evidence to the contrary, then maybe it's time to use your DM World Building Powers to adjust the rules so that they make sense. You may just find out that
Pelor is Evil.