As the author of this article states, I am not a pilot either. But I am a trained and highly experienced Avionics Technician. While I have not worked on every kind of airplane, I have worked on a large spectrum of them ranging from old dumb analog airplanes to some with fairly new glass cockpits.
I will come out and say it in plain English. It is impossible for a virus or Trojan to infect the control systems of an airplane. Those computers have custom software running in them. They are not based on windows, any flavor of the MAC OS, or even any flavor of Linux.
Any malware that would run on these systems would have to be custom written to take the place of the software that actually ran the airplane, and once it was installed in the system, it would not be able to get out to replicate itself. It would have to be done either at the manufacturers or at a repair shop. But even then it would have to pass a rigorous testing procedure.
I wrote about this a bit more here, http://spywarehammer.com/simplemachinesforum/index.php?topic=8681.msg67717#msg67717
But rest at ease. If this airplane was brought down by a problem in a computer, it was a failure of the computer, not a malware infection. But it is my experience that even a computer failure will just cause the pilot to have to fly the airplane by hand, and not rely on the computer. To the best of my knowledge ALL commercially flown airplanes in the World (for sure in all western countries) have to be landable with all electrical power out. In fact if you take away all electrical power and leave 50% of the engines running, airplanes are capable of maintaining altitude and landing safely. But even by killing all the engines, airplanes have to have backup systems that allow flap deployment, and gear deployment, which means the plane is landable. It may not be a pretty landing, and it may hurt some people a bit, but it will land, and most everyone should walk away.