Specifically, each of DC's four main superheroic generations was represented by a signature super-team. The Justice Society was followed by the Justice League and its sidekicks, the original Teen Titans; and (eventually) the Titans' own successors. We can picture this progression in terms of the Flash legacy, from Jay Garrick to Barry Allen and Wally West, and then to Bart Allen.
The New 52 took a machete to much of that history. It relocated the young-again Golden Agers to an entirely different Earth-2, shunted many original Teen Titans into limbo (including Wally West) and slashed the 15-year "modern" timeline to just five years.
May 2016's Rebirth one-shot addressed these changes directly. It explained that 10 years had been "stolen" from DC-Earth's timeline, brought back a classic version of Wally West (who represented both the forgotten Teen Titans and DC's overarching legacy structure) and teased the imminent return of the Justice Society. Since then, Golden Age Flash Jay Garrick returned very briefly in the four-part "Button" crossover (June-Early July 2017's issues #21-22 of Batman and The Flash); while Doomsday Clock issue #2 hinted at roles for the Golden Age Green Lantern and the original Hourman.
Still, why drop the Golden Age generation down the memory hole in the first place? In the context of the New 52 it made the DC Universe a little less crowded and/or complicated. Besides, DC had been sidelining the JSA occasionally ever since the end of Crisis On Infinite Earths, where (ironically) they outshone the then-current Detroit-edition JLA. After going into actual Limbo in 1986's Last Days of the Justice Society special, the JSA returned in 1992's Armageddon: Inferno miniseries, and were retired again in 1994's Zero Hour. Not until 1999's JSA ongoing series would DC's first super-team get a stable spot on the publisher's schedule. Conversely, by 2011 only something as radical as the New 52 could remove the JSA from DC-Earth's timeline.
Therefore, on today's DC-Earth, superheroes are still a relatively recent phenomenon, going back only some fifteen years (assuming that stories like "Superman Reborn" have already restored the missing 10 years). Doomsday Clock's protests against the "Supermen Theory" suggest that super-people haven't been normalized to the degree they were when the JSA was part of the timeline. Even on the pre-Crisis Earth-One, the public had years to get used to the idea of Superman, because he first went public as the teenaged Superboy.
Nevertheless, for someone from Watchmen's world who sees Doctor Manhattan as the source of society's problems, any superhuman is potentially a dangerous one. As Ozymandias puts it in Watchmen issue #11, Doctor M "somehow symbolized mankind's problems. As tensions rose, the elevation of costumed heroes became a descent." This drove his plan to save the world from certain collapse, and incidentally "assume the aspect of kingly Ramses, leaving Alexander the adventurer and his trappings to gather dust."
If Doctor M himself feels the same, we suppose it makes sense to get rid of DC-Earth's Golden Agers, on the assumption that once they were gone, no replacements would arise. This probably didn't have the desired effect. Whether or not Doctor M intended it, the New 52 produced a familiar crop of super-people; and D-Clock shows Earth-DC going down a similar path of anti-superhero sentiment and potential global catastrophe.