In a word...yes!
One doesn't need to know how to fly an airliner to carry out the atrocities of 9/11. All that is required is an appreciation of flying at private level, an appreciation of airliner performance and speeds, and a detailed knowledge of how to program the flight management computer controlling the aircrafts path.
Once this is programmed it will deliver you anywhere, anytime and at any height. Today's flight simulators more than adequately provide such information for someone with the motivation to learn.
Sadly whilst they are provided primarily as games, they now provide realism in the portrayal of airborne software and hardware that makes them an easy means of education for those with evil intent. However, in the same way that banning gun ownership in the UK has seen gun crime increase iexorably ever since, do we ban flight sim's and rob many thousands of genuine, harmless enthusiasts of their much loved hobby. I think not.
Banning flight deck sims is another knee jerk reaction that would provide the yanks with some good sound bites but do nothing to increase flight safety. All you would do is drive the industry underground and make it twice as dangerous.