Quote by 1000ideen: I wonder if it would be secure enough to move only the config.php into the new subdir public_html/geeksystem/ and password protect it ? that would be easier for fantastico users.
I would actually worry more about the directories than about config.php. The backups directory invites anyone to download database backup (if they can guess or somehow find out the file name), the systems and plugins directories may contain files that could be used for spamming or even hacking your site, ... config.php is only at risk in case of a server misconfiguration.
bye, Dirk