Sir William Golding died in 1993, according to my reference book, The Riverside Dictionary of Biography, so we would have to ask what he thought of the characters he created in Lord of the Flies. According to The Riverside Dictionary of Biography, "Golding said that this book arose from his five years of war service and ten years of teaching small boys." This suggests to me that the realities of war taught him that men were only superficially civilized and that the realities of teaching small boys for ten years taught him that small boys could easily revert to savages because they were all little savages at heart. His ten years of teaching small boys may have been more harrowing than his five years of war service. Lord of the Flies is an important book because it exposes the thin veneer of civilization that exists precariously in our civilized world.
This is a great question, but it probably cannot be answered all too well. To talk about the author's intent has fallen on hard times. Moreover, in a story it is hard to know how to take things. Therefore, all we can do is make educated conjectures. In light of this, I would say that William Golding favored Ralph or Piggy the most and Jack the least. Here is my rationale.
Ralph is probably the most consistently "good" character. He has the best leadership and his decisions are most consistent with civilization. He is the one who wants to build a hut, seek order, find a plan to escape. Similarly, Golding seems to take delight in Piggy's scientific mind. He thinks of using the conch to get people together and thinks of using his glasses as a way to make fire. Perhaps William Golding felt this way, because his dad was a science teacher. Also before Golding changed his major to English literature, he was a science major at Oxford as well.
Jack is perhaps the most hated character, because he stands for brutality and chaos. It should be pointed out that Golding fought in World War II. He was in the Royal navy and was at the sinking of the German ship, Bismark. The brutality of the Germans might has influenced the character Jack.