He was mad because the governor would not let him come into the harbor, and he raised this storm in revenge.

It is a dangerous thing to interfere with the Admiral's wishes.
For you see in those days people believed in witches and spells and all kinds of fairy-book things like those, when they could not explain why things happened.

And when they could not give a good reason for some great disaster or for some stroke of bad luck, they just said: It is witchcraft; and left it so..