Roger is a boy who has natural bullying tendencies. Having been relieved of his duty of tending the signal fire in chapter 4, he heads down to the beach. Instead of just having fun in the water or on the sand, he immediately heads for the sandcastles some of the littluns have made and plows through them. Next, he follows a little boy, Henry, without being observed, and from behind a tree throws little stones at him, deliberately missing. He makes sure to keep the stones about three yards away from Henry. It's as if Henry is still protected by parents, teachers, and officers of the law, even though there is not a single adult on the island to keep him safe. Roger has been so conditioned by the authority figures in his life before coming to the island that he still does what they would tell him to do--even though they are not now physically present.
When Golding says that the civilization that had conditioned Roger "knew nothing of him," he means that no one in the civilized world, particularly Great Britain, where Roger came from, knows where the boys are. In fact, Roger's own parents, teachers, and even the policemen from where he lived may all have died. Piggy tells Ralph in chapter 1, "Didn't you hear what the pilot said? About the atom bomb? They're all dead. ... Nobody don't know we're here. Your dad don't know, nobody don't know." The civilization outside the island from which the boys have been evacuated lies in a state of destruction due to the nuclear war taking place.
With the boys alone, isolated from their civilization that is wracked by war, they must develop their own civilization, and the remnants of the conditioning from their old life will play a role in how that new society looks and whether it survives.