Last time this came up on the board that I recall, a few of us batted about the idea that WWIII changed human proclivities, skewing it towards benevolence, relative to our contemporary tendencies.
Argue whether it's plausible or realistic all you want, but it seems to me that Star Trek has always incorporated something like the premise that humanity emerged from the ashes of WWIII a more enlightened species, as if some lesson were taken to heart.
(ETA: Ninja'd by 1001001.)
From an out-of-universe perspective, that widespread benevolence could be just a natural consequence of the basic premise that the future is going to be better than the present. That basic premise, in general, was clearly something that Roddenberry et al. leveraged to make Star Trek appealing. It's worth noting that it was leveraged most successfully when the idealism was checked, or at least challenged, by dramatic necessity and pragmatism.
Additionally, as if to counterbalance any skepticism the audience had, DS9 contributed Section 31, to demonstrate that covert campaigns were still in vogue. No doubt that was part of the appeal of DS9. But arguably, approaching the universe with even more nuances and fewer simplifications was less successful than the relatively sweeping idealism of TOS and TNG.
In short, the appeal of the franchise seems to depend upon striking a balance between idealism and pragmatism. When that balance has been tipped one way or the other, the shows have lost appeal.
I can see your argument and those points regarding DS9 are interesting, to be honest I haven't got into that show yet but something tells me i'll like it.
But you are right, despite what I have mentioned about the Federation's portrayal, the stories do maintain that balance more or less. That is one of the reasons why TOS is still very watchable in 2013 and many other 1960s programs are not.