In the final scene Ralph weeps because he has lost his innocence. Why? In comparison to others, he was good.

Ralph actually weeps for three things in the final chapter of the novel:

And in the middle of them, with filthy body, matted hair, and unwiped nose, Ralph wept for the end of innocence, the darkness of man’s heart, and the fall through the air of the true, wise friend called Piggy.

Ralph has lost his innocence. He thought, at the beginning of the novel, that it was a "good island", but, by the end of the novel, has realised the truth: that the boys themselves have turned the island from an Edenic paradise into a burning, fiery hell. He has realised the "darkness of man's heart", the badness and evil within all human beings. He is aware - and he has witnessed (and, with Simon, participated in) the deaths of two young boys.

He was better behaved than some others. But he did join into the hunts, he did feel the "desire to squeeze and hurt". He failed as a chief to hold things together, and to present a viable challenge to the glamour and excitement of Jack's hunting. He didn't have the strength of Piggy or Simon, both of whom repelled the idea of the beast. The beast won out in the end, and destroyed the island.