There are several different ways to start a script as root, in rc.d, crontab, etc. Starting a script as a user however can be just as easy in crontab:

sudo vim /etc/crontab

and then add:

@reboot usernamehere /path/to/script/here

So, why do this? Security. In my case I had a public service that I run (an IRC bot) that refuses to run as root for good reason. The program will only run as a user to prevent any hacking attempts getting root easily. Never run public services as root.