The military isn't perfect, and that day, they were already intensely involved in what was occuring in New York. They are "geared" toward threats coming from outside, not inside, the country. They could track it to some extent, but that wasn't the only plane in the air without a transponder. And tracking it doesn't equate to catching in, they have planes, but that doesn't mean they have pilots immediately available. (Sort of like New Orleans and its busses - and one without the other is useless.)