The missing piece is a filesystem (FAT filesystem). The example software in the compact-flash support download on this forum gives you "raw" access to the card... not terribly useful for reading in things written by a PC.
Options available:
- google around for some open/free fat filesystem code and port it
- locate the fat spec and write your own
- try eCos -- it includes compact flash drivers, fat file system, networking, etc. Only disadvantage is that it is it is not at all automatically intergrated with the Niso II IDE/HAL/build flow.. it provides all its own. Once you have an eCos library setup and configured how you want it, you can run/debug from the IDE - but its more of a power-user thing currently.
The eCos for Nios II document included with the download also gives the basic steps to get compact flash working.