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.... Or so believes Gene Roddenberry.
We just gotta figure out what the hell happened to these dumb apes that we somehow achieved enlightment and formed the Federation.
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In every version of the story I've heard, it was a mix of two things. First, the near destruction of humanity by all the other things we have been talking about. Basically a massive war or wars that result in the deaths of tens to hundreds of millions of people and serious decade long enviromental problems worldwide.
The second is contact with aliens (the "we are not alone" ideology).
It does not end the "humans are special" mentality, because the writers are only human.
The Federation level utopia Earth did not happen over-night even with Star Trek. It still took decades after First Contact to clean up the mess from the last World War or whatever conflict trashed the human race in the mid-21st century. It took a century for humans to be mentally ready to handle being in a near-utopia where human and alien technology has ended most of the planetary populations needs (food, shelter, and power) and ended a larger amount of the crime on the planet. It was still not over certain types of xenophobia and speciism. That took yet another century even after the formation of the Federation (a result of the alliance of species against the Romulans).
By Kirk's era, Earth is a utopia and humans have "gotten over" most things. Not everything, since our species is still emotionally charged and written by 20th century writers. They are only a few mentally unstable people left and they are on isolated mental correction planets awaiting medical treatments that will correct their heads and make them more or less normal again (Captain Garth for example was reportedly healed and returned to active duty in Star Fleet a few years after his incident with Kirk and crew).
Another century passes (Picard's era) and we've almost become preachy in our utopian Federationist ideals. Only a major Intragalactic war (Deep Space Nine's Dominion War) tones us back down to Kirk era ideals and stops the preachiness of the mid-24th century Federation.