The storm amounts to a spiritual sledgehammer, finally getting the brothers’ attention. Only when the situation was absolutely desperate did they make a connection between their plight and the binding of Nephi. They may not even have seen that binding Nephi caused the problem, only that he had demonstrated a connection with Yahweh in the past and that they now needed divine intervention.
Nephi’s patience with his physical pain and his reaction of praise, rather than murmuring, stand in sharp contrast to his brothers.