It is a deeply ingrained belief in Christianity: God gave humans dominion over the animals, interpreted to mean we can use them for our own purposes in whatever way we choose. I think, however, that a discussion of our relationship with animals can fit into mainstream Christianity. Christian animal advocates can focus on two areas when discussing animals with fellow Christians.
Stewardship. Stewardship is a regularly discussed, mainstream concept in the Lutheran churches I've been a part of. God grants us many gifts, but they still belong to God: we are stewards of God's things, and we must be good stewards. The focus on stewardship leads directly to a Christian environmentalism: God granted us the earth, and it is our duty to take care of it and protect it, not use it up however we see fit, ultimately destroying it.
Stewardship, I believe, also leads us directly to concern for animals, for even in a mainstream Christian view, we are also stewards of the animals God created. So we can ask questions. We can be specific: is it good stewardship to cut off a chicken's beak and make it live its entire life in a very small cage? We can also be broad: is any part of the factory farming system really good stewardship of God's creations?
Compassion. I come back to this argument again and again: if you eat animals, you choose your own momentary pleasure over the life of an animal. In the modern developed world, we do not eat meat for our survival, but for tradition and for pleasure. As Christians, can we really selfishly choose our own pleasure over the life of a living creature? A creature that thinks, feels, and suffers? As we learn more about the mental and emotional capacities of animals, and as we learn more about the ways they suffer in the factory farming system, I wonder if we can set aside our basic Christian principles in order to continue our focus on superiority and dominion.