This is why I believe that it was training exercise. Perhaps to draw attention away from something else. Did you notice how Bush was conveniently away from the Whitehouse during this incident? A counter-terrorism exercise would also give the Bush administration the appearance as if it was doing something to combat terrorism in the United States in easily controlled circumstance and would allow them to frame the "War on Terror" in terms of a domestic agenda. Think about it, again the most cherished symbols of our nation came under threat today and Bush vanquished that threat.
http://www.globalsecurity.org/org/news/2005/050123-terror-fight.htmJCS Conplan 0300-97, calls for "special-mission units in extra-legal missions to combat terrorism in the United States" based on top-secret orders that are managed by the military's Joint Staff and coordinated with the military's Special Operations Command and Northern Command, which is the lead military headquarters for domestic defense." page 20:
http://www.codenames.org/ArkinsContingencyPlans.pdf