Smells like someone screwed the eff up big time. Those systems, as I understand it, are supposed to be physically isolated from extraneous connections. Perhaps a stuxnet'esque style attack, infecting outwardly connected systems and thus transportable media known to be in use in those facilities in the hope that some putz plugs said media into one of the isolated systems?
That, or the story is completely misleading and the flight control computers/sat. networks are not what were actually infected, but was really just one of the unclas computers plugged into the net.
