First, it is important to understand the imagery of the Lord of the Flies. Within the novel, the Lord of the Flies is a severed pig's head. It is impaled on a stick and offered to the beast. This symbolizes the evil within all people. We know this much because the Lord of the Flies communicates with Simon and tells him that evil lurks in people.
Now as for the pilot, he is like a second Lord of the Flies in two ways. First, the pilot is there, just there, lifeless but powerful, like the Lord of the Flies. It is a constant reminder of the evil within.
Second, what makes this even worse is that the world of adults seems to send a message confirming the depravity within people's hearts. To put it another way, there is a war in the "real world." It shows that even adults who should know better are gripped by base desires and savagery.