If I had to hazard a guess, the size threshold for screening is based on the anticipated value of the aircraft to terrorists. Small aircraft can't do as much damage as your 100 - 200 tonne passenger jets running into ground structures.
When I commented to some about the lack of security I had noticed on the aforementioned Anchorage-Kenai route, this was greeted with a general shrug and eventual dismissal with "Well, you know there really aren't that many tall buildings in Alaska."
In truth, Anchorage has a few 20-ish storey buildings that could be made a royal mess by an encounter with a Twotter or Dash 8, especially one that might be carrying a bit of extra unscreened "bang" as payload. On top of that, it's not far from a major pipeline (the Trans-Alaska) that carries something like 20 percent of the crude production of the United States.
But I guess that doesn't count...
