To add a directory to a system-protected directory. It's all about protecting the integrity of the installed system. If you don't like/want it, you can reboot into recovery, disable it, and leave it that way.
Why is this important? It's trivial to reformat my drive and have a fresh install. The stuff I have that's actually sensitive is in my home directory and still unprotected =/
My system was plenty protected already - it had a root account with a password only I knew. This is just more annoying Apple gatekeeping.
And yes, it is Apple "Gatekeeping"... the same gatekeeping that's kept OS X almost completely free of major hacks for over a decade. I don't consider that annoying but to each his own.