Of course people eat meat yet disagree with it. It's called being addicted, it's called rationalizing, it called giving in to your taste buds. It is often pointed out that if we, each of us, actually had to kill our own animals to eat, most civilized people would become vegetarians overnight. Some meat eaters can admit they're selfish, that the convenience of buying a McDonalds hamburger it is too great for them to overcome. I can actually respect those people, at least they're not kidding themselves that what is happening is all fine and dandy.
I think pet ownership is a messy subject, simply because of the waste it creates.. the strays etc who live terrible lives. I don't think domestication is itself cruel though, the relationship can be said to be one of mutual benefit or something.