How is this for a ####ty theory:
Co-pilot kills pilot, then sets plane on course for south Indian Ocean, then commits suicide and passengers can't get into the locked cockpit.
I read somewhere that there is some sort of override code for the door lock. I'm not sure if it's only known by the pilots or not. I think the example they gave in the article is if Pilot A got up to go take a dump, and Pilot B wouldn't let him back in the cockpit, Pilot B could get in via some sort of override.
I guess if it's only known by the pilots, they'd be screwed. Brings me back to an earlier question of just how secure are those cockpit doors? Could a cabin full of passengers force their way in if given a few hours or is it literally like a vault?