In truth, Gotham's bad reputation had long since become a thing of the past. Even before Brainiac descended, Gotham had already greatly cleaned up its image through tourism. After the Brainiac Government was established, although it did not exert much control over Gotham, nothing major happened there again. With its decent economic development and good accommodations, it even attracted a wave of migrant workers.
Few among the younger generation knew how Gotham had earned its once-formidable notoriety. Even if they had heard that the city used to be awful, they merely assumed it had been the gangs' doing, and that everything had improved after Brainiac wiped them out.
The older generation knew a little more, but frankly, all East Coast cities had been like that back then. Gotham was bad, sure, but was Imperial City any better? Was Miami all that great? Not to mention Chicago. They simply did not take it seriously.
As a result, Gotham's dark age had long vanished into the passage of time. It had not been discussed for ages, nor was it treated with any importance anymore.
So when something strange happened in Gotham once again, no one realized that the location of the incident might multiply the danger of the entire affair.
Take tabletop RPG rules as an example: some particularly cunning game masters would deliberately prettify the names of certain location options, making them sound harmless and inviting so they could lure players into choosing them. If they were all called something-or-other Mouth, not even an idiot would pick them.
Because anything happening in places like that had a tremendous chance of mutating. Elsewhere, at worst, you might run into two fish-men. In a place like this, you had to consider the possibility of having dinner with Cthulhu.
Gotham was such a place.