"One person is saying that it would have been very difficult for an aircraft that was not a military aircraft to get into the air space of the Pentagon."
So how does that work? You're the desperate, suicidal pilot of an aircraft you are planning to use to commit mass murder. Do you contact air traffic control, request clearance and then, when refused, cry "Damn! My plan to commit mass murder is foiled by air traffic control regulations that, if breached, will result in a complex discussion with the FAA about my license"? Or do you just push and regardless, given you've got about sixty seconds to live and, what will all the virgins and all, you won't have time to worry about the disciplinary hearing?
"It's not to do with distance, but apparently the security measures taken around the airspace of the pentagon."
Bollocks. As tHoS points out, the Pentagon is about a kilometre from DCA, Ronald Reagan airport. The airspace over central Washington is restricted, but an aircraft entering the restricted area would be less than ten miles from the Pentagon, or just over a minute's flying time. Are you seriously suggesting that the US operates an air defence system capable of responding to the transgression of controlled airspace and shooting down an aircraft over a major city - including, note, the White House? I don't dispute the technical capability (although area defence weapons capable of it wouldn't be easy to conceal) but from a command and control perspective, do you have any idea how dangerous that would be? Any aircraft being de-conflicted out of DCA, any aircraft veering off the localiser, and you have the US government shooting down a US airliner (DCA is mostly internal) over the capitol.
I suppose you might put a point defence system, like Goalkeeper, on the Pentagon. That wouldn't stop a 757 from impacting the building, though.
Arguments about the competence of the pilot are moot. He's dead. We don't know.