That's definitely a problem in some areas. I think that the fact that it is a regulated revenue generator, even if most visitors find it to be an unwelcome intrusion, is the difference. Not that I agree with that situation.
In the case of personal drones the NPS, at least, has numerous concerns. Before they were banned there were a number of cases of people flying drones around very popular tourist locations, such as Arches NP, GC etc. No injuries occurred, as far as I know, but there were complaints. As the popularity of drones increased, so did the concern that these might one day become as ubiquitous as cameras. The idea of as many drones in the air as cameras on the ground around scenic centers, even if just being used as glorified selfie sticks, was not an attractive one, either from the point of view of noise and nuisance, as well as the worry that commonplace operation over crowds would inevitably lead to crashes and injuries. So they decided to get ahead of the problem and ban them until (unless) some method of regulation and control could be implemented.
The wording of the memo banning use doesn't get into detail on those arguments, but the though process is fairly clear:
"As unmanned aircraft have become more affordable and easier to operate, they have begun to appear in some park areas. Although their use remains relatively infrequent across the National Park System, this new use has the potential to cause unacceptable impacts such as harming visitors, interfering with rescue operations, causing excessive noise, impacting viewsheds, and disturbing wildlife.[2] Recent incidents at Grand Canyon National Park,[3] Zion National Park,[4] and Mount Rushmore National Memorial[5] support the need for the required closures to enable a proper evaluation of this new use. These closures are a necessary, interim measure while this new use can be properly evaluated."
So unfortunately I think that this was kind of inevitable. They certainly could restrict that ban to the popular tourist areas, and maybe that will happen as the technology becomes more accepted and mature. But at present, if they were not banned, while the UAV community might be happy, I'm pretty sure that the major tourist sites would instantly become drone magnets and the majority of park visitors would not be as happy, and that the NPS would be getting inundated with complaints and claims. It's hard to please everyone.