I think it happened because model aircraft are primarily for hobby/recreation while drones have much more commercial use, and get used primarily outside of flying model association/clubs. The FAA defines model aircraft as small unmanned aircraft flown strictly for recreational use, that always remains within sight of the operator, and is operated "in accordance with a community-based set of safety guidelines and within the programming of a nationwide community-based organization", i.e., part of a flying model club with a set of safety standards.

It sounds arbitrary but in a sense all law seems arbitrary when you are at the boundary between legal and illegal. But it makes sense from a perspective that model aircraft have historically been flown in a voluntarily regulated way, while drones are essentially outside of that. It's actually sensible because commercial drone use has the potential to cause much much more air traffic over populated areas and in aircraft flight paths.