What user were you logged in as? No user has root privileges by default and it is not wise to give a user root privileges either. Should your system be compromised, it's much easier for them to do lots of damage.
Files in /var/www/html by default are either owned by root or apache. Sometimes, apps require that apache own the files, so that the config files can be modified, for example - installing joomla. If you want to edit the files as root, you can do this:
In gnome:
CODE
gksu program /var/www/html/filename.ext
in KDE:
CODE
kdesu program /var/www/html/filename.ext
for example. Or from command line:
CODE
su (enter root password when prompted)
program /var/www/html/filename.ext
if you want to edit using vim/nano or whatever.
MySQL will also have to be installed as root, and then you need to assign a password using mysqladmin to ensure that the root user within MySQL is protected - as by default is doesn't have a password.
If you're still having problems, please explain in more detail what you are trying to do/achieve, and then we can provide more specific instructions to help.