Conda is 100% free and open source, but is developed by Continuum, which is a company (but one that contributes heavily to many of the key components of the open-source pydata/scipy ecosystem, and whose CEO basically created numpy/scipy for the community at the expense of his academic career). Personally I have had nothing but good interactions with people from Continuum and the software they develop. They (as a company and as the individuals in it) do an incredible amount for the open source community and we all benefit from that. They seem to have worked out a sustainable model for running a company and working in/contributing to open source.

I don't know. Do you use Google Chrome, Github, RedHat, LLVM?

Even gcc (egcs) was developed by Cygnus during an important stage.