For me the issue isn't with the killing/eating of animals. Rather, it's how they are treated during their lifetime by the meat industry - which is essentially optimizing for the minimum conditions that can still provide meat that can be sold legally. I'm not a vegan by the way, but I can appreciate the moral case vegans make.

For the same reason that we now consider murder, assault and other actions that harm people morally wrong. These have also been a part of life ever since humans or other hominids roamed the earth, we just determined that they are morally wrong later on.