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).
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).