There are certainly valid criticisms of the quasi-utopian vision of society in Star Trek, but that one ship was not meant as a model or microcosm of how the whole of their society was run. Just one aspect.
That's correct, but the Enterprise was clearly written as a metaphor for the perfect society. I've also seen it referred to as such by people wanting to create the perfect society.
My perspective: I grew up in and around the military, I understand military command structures and I see them as distinct from our overall society. That doesn't mean that there is no place for that sort of structure within a society. Star Trek always appeared to me as representing that military structure within the overall structure of the Federation's society. In fact, most members of the Federation were not members of anything military-like (or so it's claimed in the show, you don't really see too much outside the ship and non-Federation planets). The ship, the Enterprise, never seemed like a metaphor for anything (the Federation, on the other hand, was clearly meant as an analog to the the US and most of Western Europe, or the direction Rodenberry thought they were headed).
> I've also seen it referred to as such by people wanting to create the perfect society.
I do not doubt that you've seen this. But I've, personally, only heard and read people reference the Federation as a perfect society, not the Enterprise. Until today.
Not much is ever seen of the Federation in ST. But the parent I replied to, and its parent, are referring to the Enterprise.
Also, when I've seen references to ST as the model of utopia, Captain Kirk is often talked about front and center. Clearly, they are referring to the society on the Enterprise.
You can also see in this article cited later in this discussion:
http://grantland.com/features/next-generation-turns-25/
with quotes like this:
"and Picard’s personification of enlightened humanism"
Although I find your criticism to be fair for TNG itself - when Roddenberry had greater creative control and the Federation began to be developer as having evolved beyond petty human desire and conflict, although there were some exceptions because sometimes the writers didn't get the memo (Barclay's OCD tendencies and Geordi keeping a holographic girlfriend come to mind) and it's just impossible to write good drama where all of the characters are just insufferably perfect. Even Superman has to have kryptonite.
But TOS is the series where McCoy is pretty openly racist towards Spock and where people get into fistfights all the time - it's a lot more grounded in plausible reality.
It's a nice fantasy, but completely unworkable.