Lets say you want to use emacs to edit a file, like the /etc/fstab, where you need root permissions to edit. in a terminal:
$ su root
$ password: verysecurepassword
$ emacs /etc/fstab
your back to your user.
lets say your in gnome and want to open nautilus, do some stuff but need root permissions.
nautilus & (the & is to make the new window "independent" it will not close when you close the console window)
and voila! you have a nautilus window with root permissions. want to run mozilla with root permissions, the same, (i dont see any reason to do so... just an example) In these examples only the new window i opened as root have root permissions, all the others stay the same. (at least in my debian woody, gnome -t unstable
) This is not windows where to do admin stuff you have to logout a user and login as admin. A single window in gnome can have different rights as others. And this is not like windows that will not allow you when you are about to do something stupid. As stated before, root = god in linux. I am also new to linux and this is one of the reasons why linux is so powerful.
There are several reasons why you dont want to work as root, if an exploit or virus (yes, there are also viruses, worms and trojans that can work under linux), gets into your sistem, you are very safe as long as you DONT work as root. And it is easier to mess something up as you might think, specially if your used to having a "MS babysitter".
for more info on viruses: http://www.securityfocus.com/infocus/1695