What makes you think we don't have an air defense system?
Posse Comitatus?
Because we essentially don't. Very few interceptor aircraft on alert. Prior to 9-11 no SAMs on alert in US. Even now only a few Avengers with Stinger and guns around high risk targets from time to time. (DC probably all the time).
That was one of the "tactical" problems on 9-11, no assets close enough to the problem to make an intercept before the targets reached their targets.