By "the Reds," Ralph means the Communists, or the Soviet Block.
Golding wrote "Lord of the Flies" in 1954, nine years after the end of World War II, in which he served. It was the time of the cold war. The threat of nuclear conflict between the Soviets and the West was very real (at least in people's minds), and Golding implies that World War III, were it to happen, would result from the hostility between the forces of democracy and communism.
In subsequent comments, Golding has suggested that the novel may be considered a fable about the weakness of democratic societies (Ralph's lot) in the face of powerful dictatorships, such as those of Hitler and Stalin (or Jack). The allusion to "reds" brings us back to that level of interpretation, giving us another, political, level of understanding of the book.
Actually, Ralph is referring to whomever the British are fighting during this time. Remember that the novel is set in the future during an atomic war. We, as an audience, are not given an actual enemy for England, but it's severe enough to warrent evacuation. In chapter 10, Ralph, Piggy, and Samneric are discusses the things they would like to have on the island now. The suggestion of a boat comes up...:
"Ralph dredged in his fading knowledge of the world.
'We might get taken prisoner by the Reds.'
Eric pushed back his hair.
'They'd be better than-'"
The boys are actually comparing what Jack and his tribe have done and are doing to what some foreign country has done to England during this future war. They are deciding who it would be worse to be captured by.