6 months before 9/11 a series created by Chris Carter as a spinoff to the X-Files called the lone gunmen aired its pilot in which the govt hijacks airplanes and flies them remotely. Also see my previous post and link regarding operation North Woods.
http://www.youtube.com/watch?v=9rsMG2hHsLo
Just because you perceive the govt to be inept does not mean that they are. There are countless secret operations performed daily. As to large scale events you realize the allies created an entire fake army to make the Germans think they were going to invade through Africa and Italy and not through France and it was kept entirely secret. Perhaps you are unaware that the atomic bomb was created entirely in secret as well. Just because you fail to believe something does not make it true. DUMB or bunkers have been kept secret for decades and require the use of many people to build. The Greenbriar Resort is one such place that was once secret.
Look at area 51. There are many theories about that location however there is little proof because *duh*secrecy. So those are just a handful of examples which sink those arguments.