Ethically speaking, we should be humane to animals because they are typically completely (or almost completely) at our mercy. We have an obligation to treat them in ways that do not constitute an abuse of our power.
This is not to say that we must not eat them or use them for things like medical research. They are lesser beings than ourselves and we are justified in using them in ways that are important to us. However, this does not mean that we should treat them badly. People who are in control of someone or something else reveal their character by the way in which they treat the things that are subordinate to them. If we abuse people or animals that we control, we are showing that we lack moral character. We are, in essence, saying that our might makes whatever we do right. This shows that we lack empathy and that we do not care for other beings.
There is no good reason for us to treat animals in inhumane ways. If we do so, we are simply showing our own lack of character. We can use animals for our own purposes, but if we are ethically and morally good, we do so in ways that are humane.