Undead and their creation has the [evil] descriptor on them or are usually some form of evil. These are not the only things in the game that are a thing without strong explanation behind the "why". In fact, simply due to undead and necromancers in general being considered evil in pop culture is a pretty simply "why". D&D thrives on a driving adversary for the players, most people tend towards good/neutral rather than evil, so having a mainstay of something to be the "bad guy" that is commonly considered by most people to be bad or evil is enough explanation for me.

If that's not for you though, Libris Mortis gives many examples of why undead can be in-universe considered evil. You've got the Atrocity Calls to Unlife theory, Negative Energy as a Supportive Force theory, Negative Energy as a Draining Force theory, Undeath as Contagion theory, and the Purposeful Reanimation theory. These exist as springboard ideas for you to just use, combine with each other, or adapt to make the most sense in your game. I think the point of the book is that there is not a singular reason for why the creation or summoning of undead is evil, but rather a combination of different reasons, perhaps differing due to cultures, practices, methodologies, etc.

In the Atrocity Calls to Unlife theory, it is specifically stated that an evil spirit powers the undead. If you're looking for a "why" that is just a catch all, there it is. The spirits that inhabit the corpse are either already evil or they are slowly corrupting a non-evil spirit in to being evil as the body converts from dead to undead.

In the Negative energy as a Supportive Force theory, it explains why the entity powered by negative energy would be evil, even though the energy itself is not inherently evil. It describes that negative energy suffuses undead, and this energy drives the hunger for consumption that all undead share, that is the drive to snuff out life. So while the negative energy is not bad, mindless undead, and even intelligent undead, are usually driven specifically to consume without remorse or without consideration for the target. Mindlessly killing innocents is an evil act, and these entities are driven to do so by the very energy that powers them.

In the Negative Energy as a Draining Force theory, you've got more support for the concept that negative energy, while not inherently evil, driving these entities is a net negative, an due to the fact that it drives these entities to conduct evil acts (wonton killing of innocents, creation of other evil entities, etc) on top of being a siphon of energy from the material to the negative energy plane (thus actively consuming and destroying the material plan without consideration) which all culminate in at the very least, the powered entity being considered irreversibly evil just due to it's very existence. The energy is not evil innately, but due to the effects it has on the thing it powers and what that thing does, the creature is evil.

Undeath as a Contagion discusses the fact that the way in which some undead reproduce is a mockery of the natural flow of life, and thus make this activity inherently evil, thus making those that perform it inherently evil.

Lastly, the Purposeful Reanimation theory explicitly discusses the difference between an undead and a flesh golem (zombie and flesh golem). The theory relies on the use or acceptance of two or more of the previous theories, that evil spirits are what inhabit undead, and they form a link/bond to the negative energy plane or are powered by negative energy. Since a flesh golem is not powered by negative energy, it does not have the same consumptive drive as something that is, thus if it goes uncontrolled, it will not default to consume. Second, it is not inhabited by an evil spirit, but an elemental spirit, again removing the innate drive to commit evil acts or preventing the spirit from slowly converting to evil as presented in the Atrocity Calls to Unlife theory.

If none of these are satisfactory to you, Libris Mortis basically gives you free reign to make up your own reason. What it doesn't do is remove the evil descriptors or the evil alignment from most undead. It's seeking to give explanations, or as it says in it's first paragraph of chapter one, "...attempts to ascertain the nature of undeath itself, presenting several theories concerning the energies that give rise to unlife."