Sometimes the Federation/Starfleet really is US ueber alles, where the supposed aliens are inferior nations or races or social classes or political ideologies or what have you. Other times, the Federation/Starfleet is more of a metaphor for true human values. When Kirk is saying we don't have to kill today, he is not reserving the killing for holidays, he is saying that despite human "nature," the enlightened mind can choose the path of virtue, which is not even a sacrifice but the real path to happiness. This presupposes the notion of true moral knowledge.
Some people deny the possibility of such a moral authority. A story which does not elaborately justify the ethical presumption is regarded as failing to come to grips with the thematic content, thrusting it upon the viewer. These viewers, and those who simply do not agree with humanitarian values, feel themselves being attacked by those stories. The notion that virtuous people could be happy people offends their deep rooted belief in the actual necessity of strife and struggle and wicked deeds. And that virtue is not how people get along and live better because they get along, but a chain on their free spirit and a sacrifice of pleasure.
Modern Trek in general tended towards this view (modern being, near as I can tell, everything after the Klingons were turned into cool dudes, unencumbered with excessive intellect, instead of being a gentle satire on militarism.) It tended to give more and more lip service to noninterference, nonjudgmentalism, equal validity of all views and similar claptrap. My opinion is that this idiocy deeply weakened modern Trek's thematic honesty.
Voyager coped best I think by occasionally focusing on very basic themes of death, and the value of art, where a limited understanding of real people in real societies had less damaging effects. (And by emphasizing humor, even frivolity.) DS9 did appear to buy into the bullshit more. It is no accident that the Klingons and the Ferengi, by any rational lights both impossible and disgusting societies, were mostly adored by DS9. Or that religion was uniformly regarded as a totally unifying force, free of sectarianism, or even much boring talk of theology!
While the Founders and the Vortas and the Jem Ha'dar and, essentially, the Cardassians were regarded as pretty uniformly evil, just because.
What it boils down to, is a drama based on Social Darwinian or religious morality assumptions truer about reality than one based on enlightenment assumptions about human equality? History says the latter.
Some people deny the possibility of such a moral authority. A story which does not elaborately justify the ethical presumption is regarded as failing to come to grips with the thematic content, thrusting it upon the viewer. These viewers, and those who simply do not agree with humanitarian values, feel themselves being attacked by those stories. The notion that virtuous people could be happy people offends their deep rooted belief in the actual necessity of strife and struggle and wicked deeds. And that virtue is not how people get along and live better because they get along, but a chain on their free spirit and a sacrifice of pleasure.
Modern Trek in general tended towards this view (modern being, near as I can tell, everything after the Klingons were turned into cool dudes, unencumbered with excessive intellect, instead of being a gentle satire on militarism.) It tended to give more and more lip service to noninterference, nonjudgmentalism, equal validity of all views and similar claptrap. My opinion is that this idiocy deeply weakened modern Trek's thematic honesty.
Voyager coped best I think by occasionally focusing on very basic themes of death, and the value of art, where a limited understanding of real people in real societies had less damaging effects. (And by emphasizing humor, even frivolity.) DS9 did appear to buy into the bullshit more. It is no accident that the Klingons and the Ferengi, by any rational lights both impossible and disgusting societies, were mostly adored by DS9. Or that religion was uniformly regarded as a totally unifying force, free of sectarianism, or even much boring talk of theology!

What it boils down to, is a drama based on Social Darwinian or religious morality assumptions truer about reality than one based on enlightenment assumptions about human equality? History says the latter.