He was cold and upset. Being tied up in the water for hours was really taking a toll on him. Christine had kissed that dreadful man and, for some reason, now he was letting them go. Though Raoul hated the Phantom, he was grateful for that. He hated the thought of dying shivering and strangled in a cellar.
And so, when he made eye contact with the monster on his way to get to the gondola, despite his fear, he gave the tiniest of nods.
If only for a second, he could see the pain in the monster, no, man's eyes. And for that short moment, he understood. He saw the pain that the Phantom was putting himself through by letting Christine go. He saw. And he pitied him. For such a brief moment, he pitied him.