First off, people can't look at your website with an FTP program without login information.
They don't even need an FTP program in some cases! That links to an insecure directory on my website and you should get a contents listing in your browser no problem - its parent is set up a litte better, with an index.html file of its own that redirects to the main site (try it). Give directories index pages to stop casual snooping - as Google can be directed to search individual sites I guess you would have to write a robots.txt file to keep important files behind a veil of secrecy.