A package manager that only handles a subset of the software, in its own part of the filesystem, while duplicating a bunch a of libraries already installed is not "The package manager". It's a crutch.
It informs me when the package it's installing is a duplicate of an OSX package; I can decide if it's worth it on a case-by-case basis. By installing in a separate directory and symlinking into `/usr/local/bin`, it's cleanly separated and easy to nuke at any time. Oh, plus the ability to find problems across all packages with `brew doctor`; it's actually helped me fix problems.
If it's a crutch, it's a damn useful crutch that I can't live without on OSX, and that I'd use over any other package manager on OSX in a heartbeat.
Homebrew The missing package manager for OS X