The sound quality is often terrible, and this being radio they could have easily done this over high quality phone.
But I'm sure NPR gets "support" from Microsoft for this.
How soon before "Joan Smith joins us via Verizon, with her LG phone."
This sounds like extremely weak evidence that NPR is getting paid by Microsoft. Maybe they're just saying "via Skype" because the call is, in fact, via Skype, or to explain the poor sound quality?
I doubt "satellite" was paying them to say it
Especially if the benign explanation is as believable as it is here: Skype has simply become a word of common usage.
Journalists operate in the real world. They will use brand names to the same extend that evreryone does. Artificially avoiding them would limit their ability to tell stories as much as avoiding words that start with the letter H would.