What is funny is that Github is footing the bill for most package systems, which were likely inspired by ruby gems, yet Github itself was built with Ruby gems. I am pretty sure the hosting costs for homebrew/npm round to nil (I could be wrong).
Why do you say GitHub is footing the bill? I understand for Homebrew since it uses GitHub repositories, but npm is served via a CouchDB instance which I believe is sponsored by Joyent.