Whether the threat is real or perceived, the end result is the exact same. Society blames a particular trait shared by a group of people even though a very small percentage of those people pose any sort of threat due to that trait. Gay people were literally killed because of that perceived threat. And often no one was punished.
You also have to remember the time when this movie was released. Gay people had only just started being accepted, and there was a concerted effort by certain religious groups to try to derail any legal recognition of gay people. Don't Ask, Don't Tell was still a very real thing in the military. The entire trilogy is an allegory for gay people. The original comics may have been about race, but these movies were for a different audience. It was a commentary on exactly what was happening during that time.
You can criticize the sloppy writing of the third movie, but don't dismiss the efforts by people trying to get a message across to the general population.