Right. The OS X image now has to contain a /usr/local directory so that it exists unrestricted after you install the OS (otherwise you would be unable to create it yourself, because /usr is restricted). It has to ship with some permissions, so it rightly ships owned by root. The installer will apply these permissions each time it runs.

Aside: I really wish Homebrew didn't encourage having a single user own /usr/local. If they're going to insist on never needing sudo to install things, it should just default to installing in your home directory.

Hmm, having been on El Capitan since the first beta, this hasn't happened. Do you have anywhere it states that?