One answer I have received to the question about "why is it perfectly moral to eat animals", was that the ecology balance in nature would break down if humanity suddenly stopped eating meat. Not only have we forced our self to be part of almost everything, but our actions have cemented us to a central position. Farmers has chased away predators to the point where hunters are needed to maintain balance in many forests. Some lakes are so polluted with nutrients, that you need to maintain fishing just to keep some species from extincting other less common fish species.
This doesn't address however why breeding animals for meat is fine. This is speculation, but some local farmers might say that as long the animal can live a happy life, then why shouldn't we eat them. The farmer job is to maintain a happy flock of chickens/cows/turkeys, and makes sure it stay healthy and in appropriate size. If they do that, then morality should be on their side.
Farms that do not maintain a happy flock, or farmers that exploit and treat animals cruelly should not be allowed to have animals. We do not need to stop eating meat to get this result, as it just common sense. If a person beats their dog, or strangle kittens, we do not propose to stop allowing people to have cats or dogs. We just put the cat strangler in jail, or have large fines applied to the guilty person. The problem regarding "factory farming" is that we do not enforce such policy.