My guess is because both Operating Systems are very different, from the kernel to file systems and general architecture. Since the kernel is the part of the OS responsible for interacting with the hardware, it really does not matter much which type of hardware it is, but the OS (exception here, of course). With that said, that's why Linux programs does not run on Windows. Heck, even programs made for Windows 9x sometimes won't run well (if at all) under WinXP/2k, especially drivers and the like.
There are other reasons as well. For example, DirectX games. Since DirectX is available only for Windows, DirectX games will not run under MacOSX. The same goes to a wide range of applications that depends on a higher API to run, for example, GAIM won't run on MacOSX unless you have the GTK libraries installed.
Well... this reply is based on absolutely nothing, so I could be very off ^^
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