Well, without physical access to the vehicle it seems unlikely that malware could allow unlimited control of a vehicle. Ensuring firmware is genuine and that certain rules are stored on a read-only part of the memory would be helpful, such as don't hit people, turn off vehicle if issued a certain command.
It is good to think about these situations to enable safeguards to be preemptively put in place.
Autonomous vehicles aren't necessarily able to be remotely controlled, the computers and guidance systems are built into the vehicle, waypoints that would be located on roads would be used, which would be unable to cause damage other than the goods not being delivered and the truck being in the wrong place.
Even after 9/11 planes are still somewhat of a threat if the attacker is determined enough. Spend years becoming a pilot or flight crew and you'd have access to the cockpit, after that there's not much limit to how much damage you could cause. There is some protection at certain spots though, the White House is fairly safe: http://cryptome.org/eyeball/wh-missile/pict0.jpg