The real problem is that regional and major routes all intersect at major airports. The regionals come in to the same terminal, so Fred decants from a Dash-8 and go straight into the lounge to transfer onto a 737 to haul across the country. Fred is carrying something nasty which he carried onto the regional with the 6 other passengers and is now not re-screened before he gets onto the bigger aircraft.
Frankly the solution is to re-screen transit passengers from regionals before they get into the lounge (just like every major international terminal does when the source and destination countries screening rules are incompatible), but that would upset the major terminals / airlines (read cause them extra cost which the can, but won't bear) so they push it out to the regions and put them out of business.
A bit the same as when members of ICAO loosened the ban on metal knives on aircraft, but as Qantas had years worth of stock of plastic knives they strong-armed CASA into keeping the regulation to force their use.
There ya go, I've entered the realm of conspiracy theory and the devolution of the thread is complete.

