I would argue that this utopian society never existed in the ST universe. The Federation seemed to always be at war with the Klingons or the Romulans or whatever alien race they came across that week... Captain Kirk was more likely to shoot first and ask questions later than discuss any great utopian ideas.
Oh crap! I thought the remastering only changed the graphics!
Sure, I agree that Star Trek is not a traditional utopia. In fact I think it worth redefining "utopian" in the context of Star Trek to mean a marked social improvement compared to the period in which the series was produced, or in some ways today for that matter, not as an indication of perfection since we know that wasn’t the case. In that way "utopian" is not about lack of conflict, but how Star Fleet or the Federation reacts in those situations. At least most of the time.
It seems to me there is obviously a reason so many people feel it is "utopian". A number of actions, inferences and actual statements, such as those in the example below.
Further, Kirk obviously was not the kind of Captain to "shoot first and ask questions later". In fact that is a complaint I have against NuKirk, who does seem a little trigger happy. Maybe that's the source of confusion? Actually, on one notable occasion I recall Kirk Prime being encouraged to do what you suggest by some young hothead and his response was to point out that the Enterprise was not a democracy. Ring a bell?
Actually, Kirk did discuss great utopian ideas. Please see "Dagger of the Mind" for starters. The Federation’s penal institutions are so enlightened they put us to shame now (not hard to do), let-a-lone in the 60’s. You would almost think they were run by Vulcans.
There was a utopian vision in this one.
I didn’t see it. If fact we didn’t get to see much of Federation society except the confirmation that child raising is no better in this future that it is now.
There are large chunks of this movie without a bad guy.
Don’t recall too many of those either. Spock’s young tormentors are hardly good guys and then we see young Kirk converting and destroying a classic car while disobeying the police. Older Kirk is an "improvement", but far worse are the undisciplined thugs he meets in the bar who have unaccountably managed to steal Star Fleet uniforms.

Even after the academy Kirk’s still treating women badly and cheating on a test! Ironically, the only time the authorities make an issue out of someone’s bad behaviour in the movie and I don’t think it’s ever actually resolved, unless you count offically giving Kirk the Enterprise!
Then Spock is shown to have a relationship involving an obvious potential conflict of interest. Its debatable whether a conflict actually occured. Regardless I really can’t imagine how that got into the film. I’ll give you the Delta Vega scene but the first thing Kirk does when he gets back to the Enterprise (after saving Scotty from the plumbing) is undermine his captain so he can grab the big seat for himself. We never got to find out if that was a necessary evil because he didn’t bother trying to convince Spock that his new intel gave them an edge (or at least a chance). Finally, the behaviour of both Kirk and Spock after Nero’s defeat is well known and not "normal" for TOS (TV or movies).
As far as Uhura is concerned, I have to agree with those who are not that impressed by seeing a portrayal which seems like standard procedure these days. Obviously there will be some exceptions in the less "civilised" parts of the world.
Overall I get the feeling the movie is just "now" (or even in one case, the 1960's) with spaceships.