It was always my asumption that it was because of the Borg and that slice of the ship that they started assimilating. They had those 18 people, decided to hook them up to the network and then gained Starfleet's sense of "assimilation" of cultures. Which is mostly what it is they seem to do. (Though less severely than the Borg do) And Starfleet has a sense of trying to "perfect" themselves and unify the galaxy under those protections.
So the strong ideals drilled into the heads of those 18 Starfleet/Federation officers infected the Borg so they went out and did just that and took the idea too far.
It was perfect and harmonious. Beautiful, really.
Then Voyager came and fucked that notion all up.