But then that would mean animals have the same rights as humans. Which clearly isn't the case.

Besides if we didn't domesticate animals in the first place then there wouldn't be a human civilization to complain about the domestication of animals as being wrong. At least a civilization to the extent we have it today, just imagine if they never had horses for travel, no oxen to help till fields, no meat to eat to get protein (back before we knew anything about how to substitute meat to get protein).