Yes. If he set up an FTP site, then the place where you upload the files is not part of the system that serves up web pages. The system admin is the only one that can add permissions for people to access the FTP site, so giving people a link is not going to do oyu any good, unless the admin gives them access also. But they are going to have access to everything then.
If you just want a file storage site that you can choose with whom to share files, then I suggest Windows Skydrive
. You get 25 gigs of free storage, and you can choose who has access to a particular file. You will need a free Windows Live id.