I have a Macbook Pro and use the media keys (play/pause, skip, volume) extensively when listening to iTunes. I recently noticed that the media keys stopped working. I tried the standard things like restarting iTunes and rebooting. A few weeks back I upgraded to El Capitan (OSX 10.11). I was a bit skeptical of that being the issue since iTunes is a core part of OSX but you never know.
I did some Google searches that pointed at options in Accessibility solving the issue. None of these solutions worked. Finally I came upon this post on the Mac Rumors forums. I remembered a few weeks back installing the Google Music extension in Chrome; likely in a moment of weakness. I disabled that Chrome extension and BOOM my media keys started working again.