How to Program Hynix flash memory?

It is true that non-CFI flash devices are not supported by the Nios II flash programmer.

However, if you can get your program content into a binary format, using nios2-elf-objcopy or some equivalent, I think you should be able to have it linked in as a data section of your own "non-CFI flash programmer" routine using the Gnu "INCBIN" assembly directive. From there, your flash programmer software, including the program content with which you are trying to load flash, can be downloaded to Nios II using the IDE. Then all the programming routine needs to do is start grabbing words from the offset of the binary image you included with INCBIN, and programming them into flash. You can find details on use of the INCBIN directive in the file C:\altera\kits\nios2\documents\gnu-tools\binutils\as.html in your Nios II install.