I think it's just a question of bringing an end to your story. These characters have such an expansive rogues' gallery that you want to be able to tackle several of them, and particularly insofar as the villain often drives the plot, vary the kind of story you're telling. (After seeing "Superman Returns," I know I certainly wished Luthor had been killed in the original.) And if your villain is quite powerful, then he or she should continue to pose a threat as long as they exist; if still alive, you'll have to account for why they no longer seem to pose a danger.
I don't know, however, that it's true that villains have been dropping like flies--plenty of them have survived in one way or another. The X-Men films kept Magneto alive across the entire trilogy and beyond, as well as Mystique and Pyro; Doom is likewise a constant presence in the Fantastic Four films. Daredevil didn't kill either Bullseye or Kingpin. Sandman survives the third Spider-Man film. Schumaker's Batmen only killed two out of five villains (Riddler, Poison Ivy and Freeze survive their films, although Riddler is now insane), while Nolan's allow Scarecrow to survive both and spare the Joker. Luthor seems impossible to get rid of. I think that makes a substantial portion of surviving supervillains.
Fictitiously yours, Trent Roman