If you have enabled the root account in your fedora 16 then may be you won't able to use vlc player as root
But i tired enough to play vlc as root but I couldn't. After googling of 1 hour. I found a solution to play vlc in root account.
1. Download Ghex , this is hex editor, then open it by typing "ghex" in the terminal
2. go to file, and open the "vlc" file in the hexedittor, you can find vlc file in the "/usr/bin/vlc"
then you will see two panel right and left. avoid left panel bcoz its hex values. go to right panel and scroll down little bit find "getguid" and then replace it by "getppid" and save it. Just insert double "pp" instead of gu
after this open the terminal again and type "vlc"
I have also tested in BT5 and ubuntu