Platforms I guess. Plain C code is much more portable than JIT and PyPy is reinventing JIT implementation as opposed to using something like LLVM, so they're much more limited in terms of supported target platforms.
Oh, my mistake -- I had assumed that it did use LLVM. Good point about portability, CPython has tons of supported targets and PyPy just a handful. Also CPython is really easy to build IMO.
LLVM isn't as widely portable as generic C, either. ARM and x86 are well supported in LLVM, but CPython runs fine on MIPS, Sparc, PPC, etc (via GCC or other C compilers).