Read the article guys?
"There are specialized OSes for this kind of thing, like Green Hills Integrity OS."
Correct. And the Intel(WindRiver) equivalent. And maybe others. And for some relatively lightweight things, maybe no real OS at all, except maybe a scheduler. But so what, it's not immediately relevant here, once you've read the article.
What the article actually says is that a central maintenance/logging computer - at HQ, on the ground - was infected. So the picture is not quite as bad as you thought, although if people died as a result, it is clearly bad enough, and will hopefully cause some serious thinking in various IT departments. (But I'm not holding my breath, because most IT departments are clueless).
"Modern avionics systems have at least three different computer control circuits built into them which are self monitoring"
Maybe so. But supposing they are all based on identical requirements and all run identical software and there ends up being a common mode failure - a failure in the design or build process, rather than a random component failure?
Or suppose some management genius has said we don't need to test this stuff in the actual target environment, we'll instrument the source and only test that - after all, it's so much quicker and cheaper testing on a PC with a different processor and different compiler. Actually building it with the real tools into the expensive target system and driving that through the relevant sequence of tests takes ages and costs a fortune.
Supposing the compiler (be it Green Hills or something else, maybe something gcc-related, maybe Gnat perhaps?) has an off day and the not-quite-correct compilation results end up on the aircraft, untested? [Ada compilers can be validated but that doesn't guarantee they always produce correct code]. In the current regulatory environment this is not a theoretical possibility, it is a near certainty in the next few years.
"Surely a plane has a log book that pilots should look at."
That would seem very sensible, but actually I'm not sure it happens. There has been a massive move towards getting rid of paper in the cockpit (see, for example, "Electronic Flight Bags", which replace a whole load of paper documents). An article describing Boeing's EFB is at
http://www.boeing.com/commercial/aeromagazine/aero_23/EFB.pdf
Page 2 has a picture of it, and one item on the display says "LOGBOOK", and logbooks are also mentioned in the description. So maybe it replaces paper logbooks? Anyone know the current status of paper logbooks on modern commercial aircraft?
It gets worse. Page 8 seems to say their EFB runs both WIndows and a DO178B-certified (look it up) Linux. Go read the PDF (it's a reprint of a magazine article so may not be 100% correct, though it was written by a Boeing employee), see if it makes sense to you. Then contact your MP, or the CAA, or whoever, and tell them how worried you are about the way things appear to be going in the industry.
Air travel looks less and less attractive year by year, and not just because of the ridiculous "security theatre" at the airports.