There were plenty of mid-east / muslim terrorists in movies pre-9/11, as much of a cliche as Russian gangsters.
With regard to putting 9/11 front and center in a Hollywood movie, I think it'd be a mistake. It's too recent, the wounds are still fresh, and any commercial treatment - CGI flames and the falling towers - would [IMHO] be pretty tawdry. 9/11 showed nearly all disaster / action movies to be hollow. Why play on that emotion now when the emotion is still real?
But I am confused and cut up, surprised that even thinking about it has had such an effect. Hollywood so rarely gets it right.
I agree with your point about a 9/11 movie--I cannot imagine Hollywood tackling the sheer evil of this horror. How would the people on the doomed planes, who perhaps suffered the longest torture, be portrayed? No, its too fresh and it cuts too deeply.