Why you shouldn't use FAT as your boot partition
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You should never consider using FAT as a boot partition. By doing so, you run the following risks:
 Anyone that can gain console access can alter system information. This can be overcome by changing the "logon locally" user right.
 Anyone that can gain access to a machine can boot from a DOS floppy and change system files.
 If any mistakes are ever made with share permissions, the machine is wide open.
People often advocate using FAT to enhance recoverability. This is totally unnecessary in Windows 2000. If you boot from the install CD and select the recover option, you will be able to mount the C: drive onto the CD after providing the administrator password. You can then access the file system as if it were a FAT file system boot from DOS.
If you run Windows NT 4, you can recover the system partition by purchasing a copy of NTFSdos ($199), which allows booting from DOS floppies and mounting the system partition.