I feel that the fact that Windows is the most popular OS is the reason for this conclusion. If Linux had the kind of market share that Microsoft does, then the situation would be reversed, with Linux being declared a threat to National Security.
I don't think that Linux could ever be called a threat to national security, because the reason for them calling MS this is because they are a "Monopoly" and since Linux is mostly free, well they would have a hard time being called a 'Monopoly'. IMO.