First, the TSA itself has admitted that there is no evidence of terrorist plots against aviation in the US[0].
Second, the circumstances under which 9/11 happened would be impossible to repeat. Plane cockpits are all but impenetrable[1] - the only reason that some of the 9/11 hijackers were successful was that the standard protocol for dealing with hijackers assumed that hijackers wanted to take the plane hostage for ransom, not use the plane as a weapon. This protocol was fixed almost immediately. (Note that United Airlines Flight 93 did not face the same fate as the other three planes, because the passengers knew what the hijackers were planning.)
Since it's impossible to take control of the cockpit as a hijacker these days, even if someone managed to bring a gun on board a flight, the most damage they could do is kill all the passengers (leaving the pilots unharmed). That is truly a horrible scenario, but that makes flying no more risky than going to the movies or going to school (eg. Newtown, Arapahoe, Boulder).
Of course, one "logical" conclusion is therefore to establish TSA-style security at every school, cinema, mall, etc... in which case we have turned the country into a police state, and we should expect the same crime rates as within federal prisons: http://www.bjs.gov/index.cfm?ty=tp&tid=194
[0] http://tsaoutofourpants.wordpress.com/2013/10/17/tsa-admits-...
[1] I believe I read another comment on Hacker News a while back in which the pilot had a heart attack after the cockpit had been locked from the inside, but before leaving the gate, and it still took the fire department almost an hour to cut through the door.