My passion is studying culture, something I've been specializing in for years (and have served as a cross-cultural consultant to multinational companies in China for almost two decades now). It is amazing, given our shared genetic and evolutionary heritage, just how much cultural diversity there is on our planet. Compare the effects of the caste system in India with egalitarian attitudes in Canada, for example.
Now, consider aliens with a completely different genetic and evolutionary heritage. The problem here is that people seem to assume that aliens may not look like us, but will still largely share our psychological motivations and ethical values.
Not necessarily. Some examples:
* Consider a race that evolved from an animal that has litters of many children. Early in their evolution, they faced a very hostile environment, with 80% of their offspring being killed, so large litters (10-12) were necessary for survival. But as they evolved, and gained greater intelligence, they were able to increase survival rates, as well. However, that would lead to rapid overpopulation and depletion of resources. In order to combat this, their culture developed a principle that once children reach the age of 1-2 years old, all but the two or three strongest are killed. Evolution could select in a direction where real 'bonding' didn't take place until later in a child's life, so there would be little sorrow or moral upset over this...in fact, in their culture, it could easily be seen as more morally abhorrent to let all the kids live, as that would selfishly lead to rapid overpopulation and destruction of natural resources. (I actually wrote a short sci-fi story based on this idea many years ago)
* Or consider a race in which, like some species of animals, there are different 'ranks' of that species that is defined at a genetic level. That is, some are genetically pre-defined as warriors (strong, fast, but not very intelligent, and instinctively obedient), laborers, leaders, etc. These are not culturally defined, but genetically defined -- that is, there are very distinct genetic differences (physically, intellectually, etc.) between the different groups.
To them, a caste system wouldn't just be normal, it would be necessary. Their laborers would lack the intellectual capacity to be leaders; their leaders would lack the physical strength to be warriors; etc. To them, a rigid stratification of society would be normal.
Now -- consider the ramifications if aliens such as this encountered humans. The moral and psychological barriers that might prohibit us from wholesale slaughter or enslavement of an intelligent alien race would be largely non-existent in these aliens.
The question of how common intelligent life is, and whether or not interstellar travel/colonization could ever be feasible, are both open questions to me, and are fascinating to consider. But I do agree with those who say that assuming that actual contact with an alien culture would be peaceful, based on the principle that an advanced technological culture must also share our moral/ethical values, is naive and most likely not true.