If you mean "Too bad they didn't choose Windows", that's easy -- think of the potential lawsuits due to viral cross-infection, data security breaches, etc. that would be possible with business people using essentially "public" Windows machines.
If you mean "Too bad they didn't choose Unix", probably it was the lack of common software apps.
If you mean "Too bad they didn't choose Mac OS X", I agree completely -- but probably Apple wouldn't sell them the necessary custom hardware components required to make Mac OS X work in non-Apple hardware. I'd love to see Apple license OS X for a wider variety of hardware, even if it all stays proprietary.
But given the above, Linux is the obvious choice.
Like I said too bad they didn’t choose an American bird or original American software, but if you want to focus on the foreign born software Linux, it already has a well documented history of crashing on Airbus flights, look it up sometime.