These were my thoughts entirely while reading the article. If I want a command line utility, I really don't want to install npm then mess with any problems with that. I want to simply 'brew install' everything like that and be done.

Sure, if I need the source of something for compilation or testing, i.e. 'pip install numpy', then having that handled by pip + virtualenv makes sense.

Besides that use case, brew should handle everything to reduce conflicts.