Small websites with low cohesion between pages can probably get away with scp or rsync and nothing else. For a more highly trafficked website, you'll hide server instances from the outside world as you update their files and configuration. But this still isn't rocket science.
What I think they mean is that if you remove a file locally, it is still probably accessible on the production machine if you just use scp to copy the files over directly. Rsync is a better option for this if you want to ensure locally removed files are in fact removed on your production machine(s).
I haven't done PHP work for almost 5-6 years, but when we did it, I had post-commit scripts set up in SVN (or was it CVS back then?) that if a commit was tagged "production" would trigger the production server to perform a fresh checkout. That was the only deploy step needed.
Funny, but you can get the same type of setup working with any language. Scp a WAR file into the appropriate Tomcat directory and your Java project is good to go (no reloading of the appserver required). Or, if you have auto-reloading of modules setup in Python, you can do the same thing.
So, this type of deployment isn't just for PHP... but with PHP it is the default (only?) method.
Small websites with low cohesion between pages can probably get away with scp or rsync and nothing else. For a more highly trafficked website, you'll hide server instances from the outside world as you update their files and configuration. But this still isn't rocket science.