I think that one could call into question the ethics behind domesticating animals in the first place, but now that it's been done we have a lot of animals in the world who couldn't possibly fend for themselves. We can either kill them off, or care for them. Actually, it was suggested by a documentary I watched that the domestic dog evolved naturally (to a point, obviously).
Certain pets do make me cringe a bit, though. Birds, for example. That one just seems a little off. When I was a kid we had a couple birds, and they were very... well, for one they were mean little shits, but they also seemed very agitated.
Of course, if you're going to condemn pet ownership then you also shouldn't eat livestock.