The True Confessions of Charlotte Doyle dramatizes the conflict between an individual (Charlotte) and an oppressive system of rules and order (Captain Jaggery's tyrannical rule). Charlotte sees for herself the kind of cruelty inflicted by Captain Jaggery's rules and regulations and even suffers personally when she's wrongfully convicted of a crime she did not commit. Charlotte and the crew are eventually able to overthrow Captain Jaggery; however, when Charlotte returns to her family, she finds the same kinds of rules in place – with no way of challenging them, this time. Ultimately, Charlotte chooses to reject the system of value that organized her former life and return to the Seahawk.
Rules are necessary for maintaining a society. Even after the captain is overthrown, a new order must be installed.
Each individual should be free to make choices and live life by his or her own rules.