‘Then the men were hugely afraid, and said to him, “What is this that you have done?” For the men knew that he was fleeing from the presence of YHWH, because he had told them.'
When the men heard that YHWH was a God of the sea they were terrified, and knowing from what he had said earlier that he was fleeing from ‘the presence of YHWH', they asked him to consider what he had done. It was now clear to them that it was because of Jonah that all this was coming on them.
To flee from the presence of YHWH did not mean that Jonah actually thought that he could get away from God. It rather indicated that he had left the land which belonged to YHWH and in which He dwelt in His temple, so that he could no longer be called into His presence (compare Genesis 4:14).