When you first bring up the file manager it asks you if you want to view hidden files, if you don't check the box it wont display a file beginning with a . (unix version of hidden)
If you don't get that box, you may have selected the skip this dialog option in the past so it doesn't popup anymore.
On my cPanel at the bottom there is a link that says "reset all interface settings" If I click that and then click the file manager, it asks me if I want to view hidden files, just put a check mark in there and you should be good..