Nope. The only reported incident of aviation GPS aiding terrorists within the United States were the infamous 9/11 attacks, and that was hardly the fault of the GPS device installed within the planes involved. Other than that, there have been no other incidents, no ballistic missiles with GPS recievers to their target, nothing along those lines—at least within America. Other countries are another issue entirely.
Civilians with perfectly innocent intentions have run into trouble with these restrictions before, however. A common one is with balloon launches, which can reach heights of 100,000 feet—higher than legal GPS recievers can work at. There are many other problems within aviation GPS as well, including a lack of signal reception in many places that are popular with civilian pilots.
For more information about the US government and its policies regarding civilian aviation use of GPS, check out the official GPS website.