NPR is a non-profit that offers all of it's reporting for free. (Their income mostly comes from donors.) Their a bit of a special case since they're happy to lose money on their online offerings.
This means that NPR cannot go around their stations directly to their audience. They simply don't have the infrastructure and resources to raise an equivalent amount of donations directly. And as a matter of preference they don't want to hurt the local stations. They like the local stations.
It puts major restrictions on their product strategy. Everything they do has to have a way to tie back to a local station, and drive donations to local stations. If they just send everyone to NPR.org, they will go out of business.
In this respect, the NYTimes is in a better position for digital. They directly own all their reader and customer relationships, so they have more freedom to innovate.