Warning! Spoilers ahead for Future State: Batman/Superman #2 by Gene Luen Yang,
Scott McDaniel and Ben Oliver!
Batman just kicked Superman out of Gotham, as Bruce Wayne wants to protect his friend from the Kryptonite-wielding Magistrate. Batman often needs to save his city alone (especially when Superman is involved) and in this case, the Magistrate is revealed to know how to use Kryptonite against the Man of Steel - and on top of that, Professor Pyg used Superman's DNA to create technology to strengthen their hold over the city. Batman is also worried that the Magistrate will kill him, but he doesn't make this admission out loud. But his fear is mostly predicated on Superman's outlook on humanity and what he brings to the table as the symbol of hope: He is too trusting.
Batman is referencing what transpired during his and Superman's investigation of a mysterious substance known as False Face Serum that originated in Gotham. Their research eventually brought them to Mr. Toad who used a Kryptonite-infused knife to put him out of commission, so they could extract his DNA to "level up" their surveillance in a grotesque way that's very characteristic of Pyg, as revealed in Future State: Batman/Superman #2 written by Gene Luen Yang with art by Scott McDaniel and Ben Oliver.
During their conversation after defeating Mr. Toad and Professor Pyg, Bruce proves why Superman's tendency of overly trusting people is detrimental to Batman's efforts to save Gotham. To Superman, the only enemy is the Magistrate. But Batman's response regarding how the Magistrate didn't invade but were invited in, implies that their adversary is much closer to home: "We let our fear, our anger, our basest instincts overrule our judgment! Individuals might lose their way, but an entire city? Come on!" In other words, Batman believes that he must not only fight the Magistrate but he must save the people of Gotham from themselves.
It's true that Superman's overly trusting nature got him in the rather unfortunate mess he later finds himself in. But the irony is that he stays true to his ideals even when things are most dire: He's restrained on an operating table and there's already an incision in his upper pelvic region. Upon waking, Superman is under the watchful gaze of Mr. Toad who accidentally removes the Kryptonite holding him in place. But rather than break free and subduing the man who almost killed him and allowed Pyg to do unspeakable things to him, Superman tries to reason with him. And it works. By the end of the issue, Mr. Toad leaves Pyg and returns to his family.
This, in turn, proves a much more existential truth than Superman not having the capability of saving Gotham. Superman's presence in Gotham may have exacerbated the situation since the Magistrate successfully utilized his DNA to aid them in their dominion over the city, but his unwavering faith in humanity culminated in a positive outcome despite the many drawbacks that ensued as a result of his overly trusting nature. Gotham needs Batman, whose negative outlook will help him in his quest to cleanse their city. Without Superman, sinister figures won't be able to take advantage of and leverage Superman's powers for their own nefarious means. But Superman's absence also means that Gotham will never truly be saved, where criminals who Batman perceives as being too far gone, can actually be saved. Instead, they will just continue to fester in their twisted ideals as they await their fate in Arkham Asylum.