So, if Superman Is vunerable to magic. Then he must have hated birthday Parties
But yeah. Kryptonite Can harm Superman, but its not like a magical Force Field that will Ward him off. The only way to kill superman is to Trap him with a Magical Force Field, and then Stab him with a Jagged Piece of Kryptonite. Lex had a good idea in the film, but it is because of Lois Lane that he was able to defeat Lex.
It also explains Superman's Near Death at the hands of Doomsday. Because I Am not mistaking, Doomsday was Partially made of Kryptonite (SpectreX Can clear this up as My details are a little sketchy). Also, some of the other Superbeings have no vulnerability to Kryptonite, Like Superboy (again, SpectreX can clear this up.) as superboy has, or atleast in some comics, a Magical Force Field which gives him the near invinciblity.