I've heard that the first few years of flightaware they made most of their money in taking requests for not publishing specific aircraft. As for military stuff

I've heard that the first few years of flightaware they made most of their money in taking requests for not publishing specific aircraft. As for military stuff - they have additional capabilities for their transponders that provide for responding to interrogators (think identify friend or foe - IFF systems). They're not supposed to disable transponders in the required airspace - they've got to comply with the FAA rules too. There are situations where ATC transfers control over to the military where they are free to do more things. Like in a hot military operating area (MOA) or when ATC transfers traffic separation to the military (MARSA).