In the early part of the novel, Charlotte is in danger because she is a potential witness to mutiny. The crew intends to rebel against Captain Jaggery, but Charlotte's presence is a complication because she is unlikely to support them in their mutiny, so they either have to kill her or let a witness to their crime live. This danger is what leads Zachariah to give her the dirk and try to persuade her that Captain Jaggery is not a good man. She will be safer with the weapon and with an accurate understanding of what sort of person Jaggery is, especially because she is in danger from Jaggery as well. He is not the type of man to take anything for granted, and if she seems to pose a threat to him, he will not have any qualms about trying to get rid of her. So, all in all, given that she is in danger from multiple sides, it is better for her to have a weapon, as Zachariah persists in telling her. It turns out that he is right.