I havent read the comic books, but what you see as an addition to Woodbury, the Governor it seems sees them as a threat.
I would think its because...where the did the military guys come from?! It would seem there *IS* a government still in effect, somewhere, to be sending out National Guardsmen around in choppers. The Governor, as was implied, enjoys his power immensely and if it were to come out that there is another civilization out there, he wouldnt have the monopoly in power he currently wields.
Also, from what I can tell, the chopper did not malfunction and go down. It was shot down by small arms fire (unrealistic obviously, unless we're talking about a Barret 50 cal hitting the engine of a moving, flying target...that would be a one in a billion shot). Thats why the Governor and his men were so quick to the crash site. They shot it down.
A lot more going on with Woodbury than meets the eye.