I will not add anything to the speculations on this thread, and I am for sure not suspecting that computer security issues are the source of the problem.
I am not a pilot, but I am an active researcher in the area of computer security, and I want to add my two cents. While it may be science fiction to think of a plane being remotely controlled by an attacker, the possibility of vulnerabilities allowing for serious damage to a modern aircraft is a serious possibility.
Our community has been very successful in surfacing a number of vulnerabilities in modern cars. It is for instance possible to seriously endanger the safety of the occupants by using the embedded GSM connection used for diagnostics by car manufacturers. Similarly, the brakes could be disabled via the audio system. These and many more attacks have been widely documented in the academic research community (and tested on actual cars): Some more information can for example be found on the webpage of a joint research group established by the University of Washington and the University of California, San Diego -- cf.
CAESS - Home
With airplanes being far more complex systems, it would be pretentious to expect the absence of vulnerabilities. The only barrier preventing us from finding security issues is the simple unfeasibility of obtaining a whole 777 to play with, rendering it unusable via different types of attacks. But the consensus is certainly that there has been a lack of interaction between the computer security community and the aviation industry -- add to this the fact that the 777 is an older design (in IT years) and we learnt so much about security vulnerabilities over the last 15 years.
Overall, I would never confidently claim such vulnerabilities do not exist, as such claims have always proved themselves wrong in the past. The car industry made at first similar claims, but has in the meanwhile undergone massive investments to improve the situation after the above attacks have been exhibited 4 years ago.
Hope this puts things into perspective a bit better.