Charging per-module like github would encourage people to author fewer packages and to lump more functionality into the same package, which goes completely against the ethos of npm and the spirit of tiny abstractions that do one thing well.

The way that npm has structured things, programmers pay once for membership in a commercial tier, where presumably money is already changing hands to work on private code. I think this makes much more sense and won't bias the code itself in a negative direction.