I believe that the authorities' viewpoint is that freighter aircraft can sit about in less regulated areas of airports with the doors open, the staff who load them up could also be suspect, and it is possible to hide in a freight container - also, the A/C makes as big a hole with freight as it would with pax onboard, so it is just as desirable as an airborne missile.
That said, it's easier to secure a freight compartment - you just need emergency access in case of fire or chemical leaks, etc. A one-way door, possibly??