Earlier quoted context omitted.
Homebrew installs in /usr/local, not in /usr, and OS updates never touch /usr/local. And if you're paranoid, you can instruct Homebrew to install somewhere else instead.
It's a good idea to install elsewhere, because there are other packages that install into /usr/local (TeX, for example) that aren't in homebrew. I like having my homebrew installation totally separate -- I feel significantly more comfortable upgrading my software to bleeding edge versions if there's no chance of some non-homebrew brain-dead configure script grabbing them. I install to ~/.homebrew, and everything work…
However, if everything you're installing that depends on Homebrew-provided software is also installed through Homebrew, then it should work regardless of location (I say "should" because I suspect that not every single Homebrew formula has actually been tested with a non-/usr/local install path).
Personally, I stick with /usr/local both because I've never had a problem with it, and because that makes it easier when working with software that uses a default PATH (since /usr/local is usually put in these default PATHs). But if you have any concerns whatsoever, then by all means use a different install prefix.