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.
"Apple documentation hints that /usr/local will be returned to root:wheel restricted permissions on every OS X update; Homebrew will be adding a brew doctor check to warn you when this happens in the near future."
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.