I had exactly the opposite experience. Homebrew chewed up my computer a couple times back when it installed everything alongside OS files. The only sane way to get rid of it was to reinstall the OS.
Since the start Homebrew installed in /usr/local instead of a dedicated directory (which it now does); it literally always had a worse design than the earlier systems Fink and MacPorts. The only reason people used it is that it was written in Ruby and at the time there was a generation of new Rails developers that for some reason only wanted to use tools written in Ruby.
Not sure. It made the system binary folders user writable. It stopped doing that when Apple forced them by adding some extra security measures around /usr/bin.
Man, that blows. I find the current model (and only one I can remember? Maybe I did use it when it worked that way, and just didn't realize it) of keeping all user packages totally separate from the core system and just linking them in better and safer than what e.g. most Linux package managers do—now that I'm used to my package manager not really being able to mess up my base system, I wish all the rest worked that way, too :-/
