Golding never directly says where the boys were going in the novel, but the reader can draw conclusions based on the information and details that the author does provide. The boys in the story are English school boys, and were more than likely being evacuated from their home country to escape the possibility of atomic warfare, which Piggy hysterically mentions to Ralph at the beginning of the first chapter:
"Not them. Didn't you hear what the pilot said? About the atom bomb? They're all dead" (14).
Later in the first chapter when Jack and the choir boys are introduced, Jack mentions the plane's stopping points when he makes fun of Simon's sickness:
"'He's always throwing a faint,' said Merridew. 'He did in Gib.; and Addis; and at matins over the precentor'" (20).
Jack's reference contains some pertinent geographical information about the boys' plane route. From England, they flew to a refueling station in Gibraltar (Spain) and then on to Addis Ababa (Ethiopia); if you make a straight line between these two locations, that same line travels on toward Australia, which more than likely was the boys' destination. Australia would be a logical evacuation site; the country is far from Europe, but is still British (part of the Commonwealth).
The setting of the novel takes place around the 1950s during an atomic world war. The plane that the boys are flying in crash-lands on an uninhabited island in the middle of the Pacific Ocean. William Golding also does not reveal the plane's destination in the novel. One can infer several possibilities in regards to where the boys were traveling. It is possible that the group of schoolboys were being evacuated to Australia, Hawaii, or the United States. As was mentioned in the previous answer, Australia is a likely destination being that it is part of the British Commonwealth. Since the United States was one of Britain's allies during WWII, they could possibly be traveling to Hawaii or California. Essentially, William Golding did not find it important to reveal the location of the boys' destination and simply needed a scenario where young boys were able to create a society without the influence of adults.
They were being evacuated from their boarding school in England were being sent to a safer place, possibly the United States since they were crossing the Pacific Ocean.