There's a great article about the ethics of eating meat (and other alternatives) here.
Here is an excerpt:
"With all the problems facing humanity — war, terrorism, poverty, tyranny — you probably don't worry much about whether it's right or wrong to eat meat. That's understandable. Every society lives with two kinds of moral problems: the ones it's ready to face, and the ones that will become clear or compelling only in retrospect. Animal sacrifice, human sacrifice, slavery, the subjugation of women — many traditions seem normal and indispensable until we're ready, morally and economically, to move beyond them.
The case for eating meat is like the case for other traditions: It's natural, it's necessary, and there's nothing wrong with it. But sometimes, we're mistaken. We used to think we were the only creatures that could manipulate grammar, make sophisticated plans or recognize names out of context. In the past month, we've discovered the same skills in birds and dolphins. In recent years, we've learned that crows fashion leaves and metal into tools. Pigeons deceive each other. Rats run mazes in their dreams. Dolphins teach their young to use sponges as protection. Chimps can pick locks. Parrots can work with numbers. Dogs can learn words from context. We thought animals weren't smart enough to deserve protection. It turns out we weren't smart enough to realize they do."