It's a distinction with a difference. And no, I could not make the same argument about Planet Money, since that show
is produced by NPR.
If you say "American public radio", do you also include Democracy Now? Do you include shows produced by other local stations, including the ones that do not get distributed? NPR is not the totality of "American public radio".
Understanding the structure of public broadcasting in the USA is critical to understand why it works the way that it does. NPR is a distinct organization, even from CPB (Corporation for Public Broadcasting), even if its sensibilities are echoed in other public radio organizations (like MPR/APM).
As for your points about Adam Davidson, I don't find that shameproject.com page particularly persuasive. It's clear that Davidson's worldview does not align with that of the people/person who wrote the page/manages the site. I don't find this particularly remarkable or even particularly interesting. Davidson's worldview doesn't really line up with my own either. But there's a bunch of stuff on that page (the quotes in particular) which lack context, and a lot of other stuff that consists mostly of deeply subjective assessments and assignment of motive to Davidson without much evidence.