Will "Into Darkness" be a parable on 911 and terrorism with a message that basically says "terrorist are not really pure evil because while their methods are abhorent, their motives might be sympathetic and they only do what they do because they see themselves as the underdog?
While the Lindelof quote posted by Salvor
indicates that the writers did and do intend the destruction of Vulcan to have had an impact upon the Federation comparable in scale to that which the Sept. 11 attacks had upon the United States, I would hope that the story we get is neither so simple as a straight parable nor such an obvious parallel.
Root causes leading to terrorism generally
, now - that could work into a story in any of several ways, but there's no need for 9-11 to be a part of it - not even figuratively. It's not as if there's a shortage of other examples from which to draw.