Although one could argue there are multiple antagonists in Unbroken by Laura Hillenbrand—including the ocean and Louis Zamperini's own self-doubt—perhaps the most accurate answer would be Mutsuhiro “The Bird” Watanabe.
During Zamperini's time as a prisoner of war in the Pacific, Watanabe was responsible for the war camp where Zamperini was held. Although there is no explicit reason stated for why Watanabe had a hatred of Zamperini, a few conclusions can be made.
Because Watanabe had not been able to attain the rank of officer in the Japanese military, he despised all those who were officers in the U.S. military. Zamperini was one of those officers. Watanabe would force U.S. troops to hit their own officers in the face, perhaps because of the disdain he had for not being made an officer himself.
The main reason why Watanabe had a severe dislike for Zamperini could be because Zamperini refused to be broken by Watanbe. While Watanabe operated by invoking fear and tearing men down, Zamperini held true to his internal strength and convictions and did not cower in Watanabe's presence.
This, in turn, only angered Watanabe more and made him want to dole out more punishments on Zamperini. The two were caught up in this seemingly endless cycle of punishment and resistance throughout Zamperini's time at the camp.