There are, of course, myriad criticisms that one could level at the Federation and at Starfleet. For one, in their slavish devotion to Boldly Going Where No One Has Gone Before, Starfleet can often fail to follow up on things. On “Lower Decks,” set a good century after the events of the original series, Starfleet was finally seen following up on a civilization they liberated from a malevolent computer decades before.
For another, Starfleet also represents a set of moral and ethical values that aren’t necessarily shared by everyone in the galaxy, or even everyone in the organization. If a pre-warp society is dying of a plague that the Enterprise can cure, Starfleet ethics dictate that the people remain unaided, left to their own devices when it comes to their own fate. This, of course, goes into compicated questions on the “Star Trek” Prime Directive, itself an anti-colonialist measure.
Starfleet values togetherness and cooperation and diplomacy, but also demands from its officers a very specific code of conduct. And their code of conduct is very conservative, requiring uniforms, a respect for a military rank, following orders, and trust in the system. Starfleet officers don’t have alcohol on their ships, but booze-free synthehol. Even fraternization appears to be seen as unprofessional. Starfleet is, then, a contradiction. It’s an organization that encourages multiculturalism and welcomes outside viewpoints and intelligent interjections, but they require it under military auspices.
There are many other ways in which Starfleet can be criticized as well. But Boimler, in a moment of anger, keeps the more positive aspects of Starfleet in mind. They don’t want to flaunt their status. They are merely moved to do the right thing.