Also, what if for some reason a single machine is shared by two people and they need different versions of some programs installed with Homebrew? Installing everything in /usr/local isn't going to look like a good idea then.
A while ago I floated the idea of having a separate, low-privilege "brew" user that installs things, with the brew command automatically switching to that user, but there was no interest.
Not sure about OS X but common corporate Unix protocol is to make /home/ noexec.
Non-core ( i.e. outside central package management ) installations go to /opt/
Other than this one-liner, which is done once, there really isn't any extra hassle with using the default.
I'd be more interested in why you didn't want to install it there?
Someone I know puts it in ~/brew and that works just fine, too. His reasoning is that /usr/local/ is for all users, and though he's really the only user on his laptop, it's just wrong to install a bunch of stuff that's just for him into a global user directory.
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."