Being free of direct government funding does not make it free from editorial independence. You can listen and get an idea of their underwriting. They're clear to walk the line around a lot of topics to not upset their corporate and non profit overlords. We live in a corporatocracy and these companies and non profits are revolving doors for regulatory capture through lobbying and other methods.
A significant percentage of NPR member station funding is from individual donations, NPR is obviously also very conscious about producing the type of content its audience expects. No media outlet on planet earth is free from the influence of its audience.
If you really want to delve into how, where, and whom makes the news I suggest start by looking at the Associated Press, Agence France-Presse, and Reuters: