1. Planes often loose IFF boxes (Identification Friend or Foe - primary tracking means) for one reason or another. Voice contact keeps controllers informed and other traffic routed around problem aircraft. If nothing is heard, a search / other means of contact is initiated. Radar (skin paint) then becomes a primary means of tracking. It is difficult to track planes by radar and maintain control with peacetime / non-military controllers. These same controllers were very busy doing other things, too, during the day, not to mention a crisis. Weather, aircraft altitude, terrain masking, radar coverage, etc. all effect tracking capabilities. The reason the military cannot intercept during these situations is simple -- with few exceptions, there are no fighters on alert in CONUS during peacetime. It would take hours to scramble planes. Jets are short range, you would have to have fighters on alert all over the country to react to every potential problem. There aren't enough bases, jets, crews or $$ to do this 24/7 forever, just "in case."
2. Radical Arabs aren't the only folks who dislike our foreign policies or our allies' policies.
3. Heaven forbid, but consider this -- the FAA's grounding of all flights yesterday morning may have prevented other attacks. There is no reason to believe other aircraft that had not yet been hijacked at that point in time might not have been later, or that the bad guys will not resume their missions when flying starts again. If so, let's hope some of the passengers will get off their duffs and take prudent action before the security of another aircraft is compromised, or worse.