Just to throw out an extreme example for discussion: the Mozilla Foundation would seem to be one of the free-software organizations that RMS critiques.
One initiative they've supported is Software Carpentry: http://software-carpentry.org/scf/partners/
One of Software Carpentry's packaged lessons is for MATLAB: http://software-carpentry.org/lessons/
To be fair, the current MATLAB lesson plan includes asides for how GNU Octave can be used...but the fact that the curriculum is titled "Programming with MATLAB" certainly counts as promotion of non-free software.
Edit: by "extreme", I mean that Mozilla is in most people's minds a passionate advocate for free software, and the number of their affiliations with proprietary software lessons is extremely small as far as I can tell.
Edit 2: FWIW, RMS's definition of non-free software may be much more expansive than most people's:
https://stallman.org/airbnb.html
> Airbnb requires you to run nonfree software (an app, or Javascript). It puts you in a data base easily available to Big Brother (just like a hotel).
JavaScript is many things, but nonfree isn't one of them.