Why did Odysseus and his men not kill Polyphemus once he corned them in his cave?

The main reason would have been that it was nearly impossible to murder the giant because they had no adequate means of doing it. If they had tried to stab Polyphemus with a sharpened stake, they might have only wounded him. It was fortunate for Odysseus and his men that the giant had only one eye; otherwise, they wouldn't have even been able to blind him. He was just too big for them to kill him. Even if they had all had swords and had all attacked him at once, they still would have had a hard time killing him. But they didn't have any weapons.