According to a ruling, the heirs of Jerry Siegel will own rights to the Superman costume, the Krypton origin story, Superman's parents, and Lois Lane, among other things shortly after the next Superman film. DC / Warner Brothers will own Superman's ability to fly, Lex Luthor, and the term "kryptonite" among other things.
So what does that mean for the Man of Steel movie? IF it's a hit, I'm pretty sure Siegel's heirs will get a nice sum of money to use their parts of the character...but once this movie series is no longer profitable (or if Man of Steel flops) who knows what could happen?
After all, if the Siegel's own the costume, Superman's original powers, Lois Lane, and his origin story, they might be able to cut a deal with another studio to do a Superman (who admittedly wouldn't have the power to fly). But might all this lead to two different versions of the character? Great Caeser's Ghost!