Thanks a lot for your report. I was about to create a "Can't see course files" issue too, but luckily I searched and found this issue containing Dongsheng's explanation! I have added it to Moodle Docs - http://docs.moodle.org/en/Legacy_course_files - for others who will no doubt be asking the same question.
As Dongsheng mentions, the discussion about course files in Moodle 2.0 is ongoing, and there are still things which need to be figured out. I was also wondering about the legacy course files repository plugin, thinking it should perhaps be enabled if there are courses which have been upgraded from 1.9.
Anyway, let us follow Dongsheng's suggestion and use
MDL-23308 for further discussion, and I will mark this issue as resolved since admins can see the course files if all the steps are followed!
PS Thanks Dongsheng for your explanation and suggestion