The issue is that they are alive. they are animals, they have (at least some) thought, and they definently can feel pain. Would you feel okay if you had to kill a cow? i mean if it didnt just come in a little package at the store?
Yes, we raise these animals to kill them. But how does that justify the killing? We're killing massive amounts of animals a day! However, even that's not the issue. Humans don't _need_ meat, but it tastes great and getting all the other nutrients would be a hassle and thats lame. Im not a vegitarian, and that's not the issue.
THe issue is cruelty towards animals. Meat is cheap because the industry is cheap. And animals arent treated decently. If you want an example, just google "chicken grinder" or "baby chickens being ground up alive". It's exactly what it says it is, and it's disturbing. Male chickens wont lay eggs, and they grow much slower than female chickens. They lose money for the company, so whats the solution? put them all in a meat grinder, while they are still alive.
Basically, i dont have any issues with eating meat because i believe humans are more important than animals. However, i do not believe there is any great excuse for treating animals cruely. There are humane systems for slaughter houses, and thats great. And then there are disgusting practices like dumping thousands of new born baby chicks (while still very alive) into a running meat grinder and Animals need protection against that sort of thing.