Throughout TOS and later Star Trek series we see the Federation portrayed as a very powerful and respected intergalactic government that while is very capable of coercing many smaller and weaker civilizations into complying with their interests, they repeatedly refuse to use such means unless it is absolutely warranted or unless they themselves are already in the line of fire.
So of course these stories are set many hundreds of years from now and supposedly surround a more mature, more civilized humankind, but let's not kid ourselves here. If the Federation and Starfleet are largely or exclusively comprised of non-augmented human beings that are genetically no more advanced than we are now...how viable is the gracious benevolence of such an organization?
The most "civilized and humane" societies today continue to employ threats, back-room dealings, assassination and torture among other things in order to secure their interests and they commit such acts against other humans. Considering that we so far on a whole have no qualms in coercing our fellow humans by whatever force we deem appropriate, why would we take such lengthy measures to ensure the fair treatment of aliens who often greet us with acts of aggression?
I am not saying that a polar opposite like the Terran Empire would be any more realistic. They are simply too malicious for their own good. I will refer to the portrayal of a future human world government in Babylon 5 as something far more plausible. While they are interested in peace, they do not go out of their way to help or protect weaker species. They act as moderators but only reluctantly and only so far as their own butts would get caught in the crossfire, and they are far from sympathetic when their own economic and political positions are endangered. Sounds a lot like the great guys we elect nowadays. In comparison the Federation is Superman/Jesus incarnate spread over hundreds of starships and colonies.
Now I love TOS and Trek as a whole but whenever I see Kirk frustrated and strained, trying to negotiate with some backwater, violent and savage aliens over resources even after he has been tricked, captured, disarmed, and beaten when he could simply take what they needed without all the risk....my belief is suspended indefinitely.