I remember the scar as being the damage done to the landscape by the crashed plane. As such, the scar might be seen as a symbol of the destructive influence of humans; they have crashed into what might have been (although I don't believe it) seen as a Garden of Eden.
This question has been asked before (see the link below) and the answer given is pretty much the same as mine.
In "Lord of the Flies" the boys are being flown to someplace safe due to some type of apocalyptic disaster. On their journey their planes crashes on an island that is uninhabited. When the plane wrecks it scars the pristine environment. However, there is more significance in the symbol of this scar. The scar becomes a representation of the destruction that mankind brings to nature. This becomes even more evident later on in the story when the boys begin to demonstrate violence and destruction of one another. The beautiful island that could have been a safe haven for them leaves them scared by their own behaviors.