I listen to hours of NPR every day, and can say with very little doubt that different programs have different levels of bias. This American Life, Living on Earth, and Fresh Air, for example, are each tilted to the left (the first two being the easiest to observe) but tend to spin things subtly. In fact, you probably wouldn’t have any idea such was the case on a first time listening. Wait Wait… don’t tell me, however, is the easiest place to observe NPR bias in action. The contestants, the audience, the announcer, the panelists, the guest, everybody (except perhaps Carl Kassell) makes no secret of how they feel and, while I still love the show, I can’t help but think how much funnier it would be if Sagal and the panelists (not to mention the fickle audience who make a point of being as nasty as possible whenever it suits their ideological fancy) were occasionally evenhanded in their criticism.
As for Morning Edition and ATC, I think they both vary but are often times surprisingly able to find the coverage that fairly and accurately represents all interested parties. Their best stories are often the ones they would easily be able to fudge, but somehow present with more accuracy than I would expect from any news source.
Regardless, after years of listening to NPR, my problems are less with their occasional biases, which I automatically filter out, and more with the inadequacy of radio in general to convey accurate information in the ways other sources do.