Fly by wire
While I agree the article is probably fluff, I'd still be a bit worried about what would happen if, e.g. an attacker manages to crack into the ACARS system and from there penetrate further into the aircraft's systems.
While there's a pilot to monitor things, what would happen if the attacker manages to discharge the fire extinguishers on the engines? Or deploy the reversers during cruise? (Or just on one side - I'm sure the flight would get interesting very rapidly...)
Remember these guys who hacked a Jeep and managed to activate the brakes...
I'm just SLF, but used to work in Computer and Network security...