Earlier quoted context omitted.
It makes /usr/local owned by the current user rather than root. Not much in the way of voodoo. ;) It's basically a replacement for MacPorts.
See this section of the hierarchical filesystem guidelines for unix-like OSes: http://www.pathname.com/fhs/pub/fhs-2.3.html#THEUSRHIERARCHY and in particular: http://www.pathname.com/fhs/pub/fhs-2.3.html#USRLOCALLOCALHI... Isn't root supposed to own that?
They're guidelines.
In the case of OS X laptops, they're almost uniformly used as single-user machines. This just takes the hassle of having to sudo to do it.
There are a few other reasons they specifically opted for /usr/local instead of other paths here: https://github.com/mxcl/homebrew/wiki/installation