Without looking at how this organization works, let me clarify: a 501(c)(3) cannot be paying for software development insofar as this constitutes Product Development. Product Development is outside the scope of charitable work and, if caught, would open them up to back taxes on those 'charitable' contributions plus fines. This is not something that applies just to Matrix, but to the Free Software Foundation for that matter. Not one fucking dime you give them ever goes to software development, and the fact that they don't make this clear upfront given the obvious misunderstanding on the part of the public and what they think they're funding, is fraudulent.

TL;DR Donations to 501(c)(3)'s managing open source projects might as well be lit on fire because they do not and can not go to software development.