When Ralph hit the beach and saw the Naval officer he knew Jack's hunt of him was over, as was his time on the horror that was this island. I believe he wept partially because he was so relieved, but, as the quote says, he also cried as he thought over what he and his mates had become.
When the boys first crash landed on the island, they were pre-teen, sheltered, well-off British boarding school chaps. They relied on adults to guide them, and they had few responsibilities. Most of them had probably not seen much death in their lives, they probably didn't have to work for their food, clothing, or shelter, and most of them didn't have to worry about establishing a government or setting rules. They were "innocent."
However, within the span of their time on this island, the boys lost their carefree childhood. They had to grow up too fast, and face the fact that every man has a dark side. They witnessed death, murder, brutality, and betrayal between each other. They had lost their innocence, and would never be able to go back to the time of life when laughter and play were commonplace. He cried for his lost mates, and for how savage they had all become, and because he knew with these things in his memory, he would never be able to look at life the same again.