In terms of menace potential, any private plane will lose to a van full of fertilizer and a baddie intent on causing destruction. It's a matter of scale.
Little planes, like this one [1] just don't do damage on the same scale as airliners.
No argument though, just saying it's a hard problem, and the scaling issue makes it somewhat awkward to deploy security resources in proportion to the threat.
I don't have a solution. I'm not exactly thrilled with the current setup, but I try to stay quiet since I can't think of anything better.
Government building codes already anticipate the "van full of fertilizer" attack, as a result of the Oklahoma City bombing in 1995. Federal building security is a separate matter though, with its own agency called FPS that predates DHS and TSA by decades.
(But regardless, it’s not clear that the TSA is even performing that kind of calculus.)