How does ATC protect Air Force One?
Whenever Air Force 1 takes off or lands, the FAA establishes a 'Temporary Flight Restriction'.  

Essentially this is a big 'upside down wedding cake' of airspace in which Air Traffic Control exercises very tight control of any aircraft operating in the TFR.  Any traffic entering the TFR without prior approval, or any aircraft deviating from ATC instructions will be intercepted by military aircraft.  

When President Obama takes a bus trip the FAA establishes a TFR over the bus, that moves so as to stay over the bus as he rolls along!

Wikipedia has a good article on TFRs.