Warning: Spoilers for Batman/Superman: World's Finest #10 ahead!It may seem implausible that the relatively underpowered criminals of Gotham are able to maintain a foothold in their city when heroes like Superman are around, but it turns out that the very nature of Gotham's infrastructure blocks one of Superman's most critical abilities. Gotham's archaic infrastructure is riddled with lead lining, blocking Superman's powers of X-ray vision. This may not sound like much of an advantage, but it gives Gotham's crime lords just enough of an edge to vanish into the warrens of Gotham's underbelly.
Superman's x-ray vision is one of his more overlooked abilities, but the ability to be functionally all-seeing helps tie the rest of his powers together, pairing with his speed, flight, and strength to allow Superman to appear omnipresent. The problem arises with his inability to see through lead, which takes the form of opaque spots in his vision (as revealed in Brian Michael Bendis, John Romita Jr., Klaus Janson, and Brad Anderson's Action Comics #1024). Although this can be used to pinpoint lead-shielded items by specifically looking for blind spots, it's another matter entirely when expanded to the scope of an entire city.
This weakness is exemplified in Mark Waid, Dan Mora, and Tamara Bonvillain's Batman/Superman: World's Finest #10, stymieing the search for Batman and Superman's kidnaped ally, David. Despite the combined efforts of Batman, Superman, and the Titans in combing Gotham, progress is slow, and Superman is unable to use his vision to simply look through the entirety of Gotham at a glance. As he takes out his frustrations on an underground meth lab, Superman laments that "Gotham's overrun with lead-lined buildings -- abandoned hospitals, x-ray labs, nuclear plants, and the like." All the while, David continues to be tortured by the Joker with Superman struggling to find him, let alone save him.
Superman is Flying Blind in Gotham City.
This has huge implications for Gotham's criminal caste. For all of his powers, Superman is essentially flying blind in Gotham city, whereas Gotham's villains know all the city's hideaways and secrets. Add that to the generally unpredictable nature of Batman's rogues' gallery, and Superman is actually placed on a much more even footing with his enemies when trying to help Batman foil crime in Gotham.
The implications extend further, onto a more meta level as well: DC has a varied mix of superheroes, from intergalactic titans such as the Green Lantern Corps, to street-level vigilantes like Black Canary. Using Superman's limitations to make places like Gotham no longer safe for him to operate freely helps to explain how the noir-style environments of the street-level heroes can still exist in the same world as the Justice League. Preventing some of Superman's powers from working in Gotham just makes the DC Universe function smoothly.
Batman/Superman: World's Finest #10 is now available from DC Comics.