You simply cannot determine human nature by observing humanity today. You must realize that industrialized culture hasn’t been around for more than 200 years, and our species is over 100,000 years old (to use conservative estimates). I think over time, we've been corrupted past anything natural. The way we treat each other isn't a result of something inherent; it's from thousands and thousands of years of abuse, passed down through the ages. Of course, that's all my knowledge of psychology and anthropology talking.
As for Milgram’s experiments, they do nothing more than prove that, at the time they were taken, in the society they were taken, people have the inclination to not question authority. In our society today, we are taught from birth to obey authority, and many of us have been taught that authority figures may override our morals. The reason that some people don’t obey authority unquestioningly is twofold: 1) They weren’t just taught morals (authoritarian), but they were shown why those morals are important (authoritative) and 2) They were taught to value their individual insights and beliefs, and to simply question the intentions of others before agreeing with them simply because of who they are. I bet that if you took the San Bushmen (an egalitarian group that is slowly diminishing) out of the Kalahari Desert of Africa, and put them in the Milgram experiment, that none or few of them would keep pushing the button until the person was “dead”. It does not make sense to take more meaning out of the Milgram experiments than Milgram intended; to explain why people were brainwashed in Germany so easily. The experiment took place in a country not too different from Germany, when you get down to it. It is no less scientific to assume that minorities (i.e. black people, Latinos and American Indians) are stupid, because on average, they score lower on IQ tests. You have to take it into the societal context.
Simply put, humans are past the point of being able to blame cruel behaviors on "nature". We separate ourselves from nature and claim to be above it, and yet at the same time, say that we have no control over what nature intends for us. We must choose one or the other. And we must take responsibility for our cruelty to each other and to nature, or our species is not nearly as intelligent as we think we are.