My interpretation of the National Park Service's order is basically this:
Aerial drones are currently in their infancy. We are in a period of mass-experimentation for unmanned aerial vehicles of all shapes, sizes, and uses. There are a lot of good uses for drones, as I'm sure any Hollywood director who keeps up on recent technology could attest. It's also possible to be quite annoying with drones, such as people taping a video camera to a noisy RC helicopter and flying it around places.
The National Park Service's stance seems to be, "We understand that drones have some uses, but right now they're fairly experimental. Please do not experiment with unmanned aerial vehicles in our parks."
I imagine if there was a group, such as BBC Natural History Unit, that wanted to use some aerial drones to take footage, the NPS would be happy to give them the go-ahead. But they don't want to give everybody a blanket go-ahead.
I can understand the National Park Service's perspective. I don't necessarily agree with it, but I think I understand it.