To me it is not the suffering per se that bothers me about factory farming. I'm having trouble finding the right words, but I want to say it is the "un-naturalness" of it. Animals are not meant to live their whole lives in cages pumped full of antibiotics. I also believe it is harmful to humans, both to the humans who operate these factories (psychologically) & to the humans that consume the product (physically).

On the other hand, it is natural for animals to eat other animals, and properly raised animal products are arguably one of the best sources of nutrition for humans. I also don't think raising chickens on an open farm & slaughtering them is psychologically harmful; I imagine those farmers feel deeply in tune with nature & at peace with their way of life.