Our server stores your Web site files and your home directory in different places. When you login to either of these places with an FTP program, you are restricted to that directory and the directories below it.
This greatly improves the security of our servers. It also makes it far easier to publish Web site files without worrying about using the correct "path".
However, a side-effect of this is that when you connect to the Web site directory, you can't see the home directory files, and vice versa. To view the home directory, you need to create an extra FTP account with access to the home directory.
(Note that this problem does not occur if you use SFTP. That's because an SFTP connection is not restricted to a certain directory.)