One thing that has struck me over the years about Star Trek is how the optimism is viewed by fans. Its often said that the Federation has evolved into a Utopian society. However, you will notice that there is absolutely no Utopia outside the Federation. It is filled with savage barbarians, cold calculating beings, and untold numbers of dangers. It is the exceptional crew of the Enterprise (or other ship/station/etc..) that brings light to the darkness. Even when the heroes are wrong, they quickly reverse course and save the day.
You mess with that "exceptional" idea and things start to get real difficult to accept for some of these folks. When you realize that simply being a Federation citizen, and simply being a crew member of the Enterprise, doesnt make one exceptional alone. However, we the viewers are often only given the perspective of the Federation and its Starfleet officers, that we dont have a nuanced perspective. Enter DS9, and suddenly things are not neat, bright, and correct. The source of conflict is both external and internal and you quickly realize there really is no utopia anywhere but where the idealist make it. Which is by far more powerful a message than exceptionalism can ever be. However, that doesnt stop a lot of folks from being very uncomfortable with that perspective.
Dont mistake me for saying NuTrek S31 is good, it isnt, but I dont think the concept of what it takes to maintain a utopian society is one that should be avoided in Star Trek either.