Part of the OS X 10.11/El Capitan changes is something called [System Integrity Protection](https://en.wikipedia.org/wiki/System_Integrity_Protection) or "SIP".
SIP prevents you from writing to many system directories such as `/usr`, `/System`&`/bin`, regardless of whether or not you are root. The Apple keynote is [here](https://developer.apple.com/videos/wwdc/2015/?id=706) if you'd like to learn more.
One of the implications of SIP is that you cannot simply create `/usr/local` if it is removed or doesn't exist for another reason. However, as noted in the keynote, Apple is leaving `/usr/local` open for developers to use, so Homebrew can still be used as expected.
Apple documentation *hints* that `/usr/local` will be returned to `root:wheel restricted` permissions on [every OS X update](https://developer.apple.com/library/mac/releasenotes/General/rn-osx-10.11/index.html). There is a `brew doctor` check in place to advise if permissions have slipped for whatever reason.