Homebrew is designed to take over your OS /usr/local directory. Not that there's much in there by default, but Homebrew's presence greatly changes the semantics of /usr/local, given that it's normally meant as a prefix for the local system administrator to install things as root into, whereas Homebrew re-assigns ownership of the whole directory structure to the user installing Homebrew (who, admittedly, is a member of the "staff" group, but still only one member on a potentially multiuser computer.)