It takes real effort to run most of the LAMP stack as root. If you don't understand Unix permissions it's not easy. Apache, mysql, (and therefore php) all run by default as a low-privileged user. I have plenty of real world experience and haven't seen apache or mysql run as root outside of embedded devices, and even that was maybe a handful of times.
But the book isn't saying "You should try to make sure your web server runs as nobody". It's saying "when you're deploying your CGI programs, take into account the fact that the web server you're deploying to likely runs as nobody".