The specifics depend on the writer, but there's some supernatural force keeping Gotham from improving. The city may have been founded by demon worshipers, Arkham Alylum might have been founded by a serial killer, and there might be chemicals from underground Lazarus Pits leaking into the water supply. It all depends on the continuity and who tells the story. Long story short, Gotham is the kind of fucked up that all the money in the world isn't going to fix.