Star Trek Into Darkness had the balls to take unpopular positions on U.S. actions and all people can do is scream it isn't enough.
Everyone supports the troops; fewer and fewer people support the wars. Now that the U.S. has been at war for 12 years and we know that there were no WMDs, it's pretty easy to look back with hindsight and say that preemptive war is not such a good idea. The message would have been courageous in 2002 when everyone in America was spoiling for the fight, not in 2013 when we've already had a belly full.
It doesn't take "balls" to take the stand eleven years too late.
The position taken on U.S. foreign policy in the film is muddled. Admiral Marcus is a renegade military man, so this does not really criticize legitimate foreign policy of the United States. That admirals should not take it upon themselves to start their own wars is a no-brainer even in a post 9-11 world. John Harrison is a terrorist which only plays into the "War on Terror" angle.
Plenty of other films have cashed in on 9-11 iconography (e.g., Cloverfield, War of the Worlds), so this isn't new ground either.
I'm fairly convinced at this point that to a certain group of fans there is simply nothing Abrams can do right, short of leaving the franchise.
And I am fairly convinced that to a certain group there is no criticism of the new films, no matter how patiently reasoned it may be, which will be tolerated.