Lord of the Flies represents what goes on in our society in several ways. First and most simply, the boys on the island have been trained and educated well. They should be able to live moral lives, and to organize a peaceful and healthy society. That they cannot points out some of the weaknesses in our civilization.
Second, individual characters represent different types of person from our society, and therefore can be read as commentary upon them.
Third, and most generally, they form a society in miniature. Therefore, what happens in their society mirrors what happens in ours (and vice versa).