Charlotte is impressed by the captain and he makes her feel special.

Although Charlotte does not realize it, the captain is clearly taking advantage of her. To her, Captain Jagger can do no wrong.  She is impressed when “all eyes upon us as we crossed the ship's waist to the bowsprit and figurehead” (Ch. 6), causing her to feel like a princess ascending to her throne.

Not even the same lowering mist I'd observed when I first came from my cabin could dampen my soaring spirits.  Captain Jaggery was a brilliant sun and I, a Juno moon, basked in reflected glory. (Ch. 6)

To Charlotte, the men on the ship are beneath her and Jaggery is closer to an equal.  He makes her feel like a princess, and treats her to all kinds of luxuries while he asks her to spy on the men for him.  He tells her they are dangerous, and tries to make sure she is on his side and not theirs.

Although there were signs that something was wrong from the beginning, Charlotte did not really notice.  She was not supposed to be the only passenger, but all of the others cancelled.  Not even the porters carrying her bags will stay near the ship.  Charlotte will discover soon enough the real truth about Jaggery.