At first I used to log in as root, while my linux knowledge was limited, and thats ok. But after a while I noticed that the whole point of the exercise is to have a stable system. If you run a program as root it then has the abiliy to alter any file on your system without any further permission from you (like windows98).
If, however, you run your system as a normal user, the only files you can muck up are in your home folder (/home/*username*) or in the temporary files folder (/tmp/*yourtempfiles*), therefore once you have got your system up and running it is rarely nessecary to work on files as root. Lets face it, if you muck up you user account, all you have to do is start again with a new user:- ctrl+alt+F6 log in as root then type "useradd" to add a new user then try again! As long as you only do specific system related tasks when logged in as root you cannot go wrong (well nearly!). Tasks such as installing/uninstalling or adjusting system setting in /etc.