The terror organisations recognise that the sure way to win the current war they're waging against the West is to use the Ronald Reagan ploy of making the war simply too expensive for the other side to wage. If this turns out to be a terroist attack, it's clever, particularly if it can be repeated.
Someone, be it a terrorist who forced his way into the cockpit or a pilot who has been recruited or forced to co-operate with the terrorists, had to have enough knowledge of the 777 to know which nav and comm. functions to disable - and in a very short time - to cause it to disappear (in an electronic sense) in a matter of seconds. After that, it's just a question of getting the aircraft a long way away from the commonsense search area before ditching it or flying it deliberately into the sea to destroy it. (When your foot soldiers are willing to die for the cause, the possibilities that can be employed are endless.)
The effect of two or three similar disappearances will be huge. The incredible expense, both to governments and airlines, in just trying to find the missing hull, will eventually become crippling; the drop off in passengers, as airline travel becomes something less than 100% safe in the public's perception, will hurt the airlines' bottom line; the increased security measures will make airline travel an even more painful experience than it has become since 2001.
All will end up making travel very, very expensive, which means the bad guys will have won, for without easy and cheap air travel, Western society will not be what it has become over the last fifty years.