Star Trek is a sci-fi universe set in the very far future that was originally created in the long past. Since the production of The Original Series many of the themes presented have become a classic in the genre, but due to the amount of copycats, today they seem just cliché. All Star Trek series are actually based on clichés, some that are only present in one series, some that are present in all of Star Trek, and some that evolve out of the show into other media. Unfortunately one of those of the last sort is the potrayal of alien species.
Story of a noble human and the savage xeno
People in Star Trek live in an utopia where all material needs are satisfied. As such, humans are virtually devoid of greed. They commit evil deeds only if they believe that they are pursuing a good goal. At least that's what Picard claims in one of the episodes in which the writers are very critical of capitalists. The show itself contradicts this statement a number of times, but either way that is how the creators want us to see the Federation — as the near socialist do-gooders.
Most of the Star Trek plot is based on people — federation officials, solving conflicts between aliens. While the former are depicted as rather good, they are not nearly as perfect as humans. Each species represents one or more human vices: Klingons (short-temperedness, corruption), Ferengi (greed), Cardassians (lack of empathy, war crimes), Vulcans (ignorance, snobbery), Romulans (treachery).
People and xenos alike are completely aware of these traits and often point them out. Of course, aliens do not consider humans perfect — a Klingon may complain that they are weak, and a Vulcan that they get carried away by emotions — but by European/Christian standards, humans as a species remain virtually flawless. Despite this, human characters often act on prejudice. Sometimes it's a part of an anti-racial commentary, but more often it's just dropped as a gag.
Furthermore, in the universe of Star Trek most aliens are shown to be extremely similar to humans in both physiology and culture. Hell, in some episodes the makeup artists get lazy and use a generic alien look for some unknown race, which is exactly the same as humans but with a bumpy forehead.
What I am ultimately getting at, is that the portrayal of alien species in Star Trek is accidentally extremely similar to how the Christian colonizers saw the natives of their colonies. The official narrative went about like this: natives are human and somewhat similar to Europeans, but they need our guidance to be as cool and religious as we are. But the road to hell is paved with good intentions. Europeans governments exploited their colonies, and colonizers exploited the indigenous population. Effects of their iron fist can be seen to this day with instability of Africa and the Americas. So yeah, in a way Star Trek treats aliens the same way the Europeans treated natives in their colonies.
So what? Star Trek bad now?
Well, not really. First of all, the Federation doesn't exploit aliens, they are the do-gooders. Star Trek is ultimately a liberal show that promotes racial tolerance through aliens. The problem is that for reasons unknown to me, the universe almost always focuses on xeno vs xeno conflicts, painting humans as flawless. An exception to this rule are the Maquis, for example. It's not like every episode of every series shows the sentiment I talked about here either, it's just that if you think about the Star Trek universe in a broader perspective, this is the sort of conclusions you can come up with. The moral of this story is simple: think about what you write.