We've gotten used to a painful, privacy invading security process when we fly. But why should we do this for shot-hop, small aircraft. Those ones on the 20 seat Canadair Business Jets and similar. Secure the cockpit with a sealed door and arm the pilot so that terrorists can't take control of the plane. Put in sealed transponders so ATC knows if the plane goes astray. Give the pilot a "disable" button that limits what can be done with the plane in the event of attempted hijack.
Other than that, give it no more security than a bus or train. Just show your ticket, or pay cash, and walk on, possibly going through no more than the metal detectors used at things like baseball games and museums. Possibly not even that.
Yes, evil people could smuggle a gun, and suicide terrorists could put a bomb in their luggage. And kill 15 people. Which would be horrible, but frankly there are a lot more dangerous targets out there for the terrorist willing to kill himself, where a lot more damage can be done, and a lot more people killed. Hell, there are more tempting targets where you don't have to kill yourself. It makes little sense to waste resources blowing up tiny planes.
Which means we should not go nuts securing them. This already takes place at small airports and on general aviation. I've seen post-911 stories of people just walking onto small corporate jets with no ID or search, as well as other private planes and charters. Combine that with other ideas on efficient plane operation and you might just have a very popular airline for flights under 500 miles.