You're right, I probably misread the question... Having quotas on subfolders, and no quota on the inbox, works. Having no quota on the inbox, though, and automatically applying a quota to new subfolders created there... well, that wouldn't.
You could, however, do this:
user.test no quota user.mail quota user.mail.folder1 (inherit) user.mail.folder2 (inherit)
etc, assuming you have a setup where it's possible to deny the user permission to create direct subfolders of the inbox. I don't know enough about Cyrus ACLs and quotas to know if this will work - it's just a suggestion. Of course, it may also be unsuitable for your environment.
Craig Ringer