The NCR is at conflict with people so they kill them, again Caesar would not kill all of them just based on their way of life he understands they do not know any better. And I believe I listed most of the tribes in F:NV, so if you have an example of a tribe that isn't destroyed by the NCR I would like to see it. Also the problem is the tribes are at a conflict with the NCR, because the NCR invades their land. This is kinda like saying that the colonists of early America where okay in murdering the Native Americans, because they acted violently to their land being taken. And you are right about the NCR population here is the wiki quote "he uses the above tactic to turn the small number of people under his command into a dedicated army capable of actually standing up to the superior numbers of the NCR."