Hi Fuji,
To make this work you'll need to do two things:
1. Make sure that the CPU reset location is set to EPCS flash. This is done in SOPC Builder in the "More CPU settings" page. After making this change you will need to re-generate in SOPC Builder and re-compile the design in Quartus, as the reset location must be compiled into hardware.
2. In the flash programmer GUI, DO select the "Program software project into flash memory", DO NOT check "Program other file into flash memory", with the .elf file.
Reason: programming the .elf file in this way will not work; the contents of the .elf are parsed by the flash programmer and only address:data records written into flash. Selecting "program software project into flash" will direct the flash programmer to do this, if the reset address is pointed to EPCS.