A few weeks back, FileZilla for some reason stopped showing .htaccess and other files and directories (starting with a period, .). I was about to give up and ditch the program, but I liked it too much and eventually got it working. If you are having these issues, try:

Support from MediaTemple (I was convinced it was their servers) told me to force the FTP program to display hidden files. With FileZilla, simply click the ‘Server‘ menu and ensure ‘Force showing hidden files’ is checked:

Check 'Force showing hidden files'

This did not solve the problem, but it is understandable that it might in some circumstances.

I’ve never heard of filters in FileZilla, but a post on FileZilla Forums advised that they be off. Sure enough, this was the problem. Simply click the ‘Filters’ icon and ensure no filters are active (uncheck all tick boxes).

Click the 'Filters' icon

Uncheck all tick boxes