"To be or not to be? That is the question." OK, fine, it's not the question here. That would be Hamlet. The question for this book might be something more along the lines of "To do or not to do?" Or maybe even "What the heck should I do?" Charlotte Doyle, you see, has a very difficult time trusting herself to do much of anything. And why should she? She's a very young girl, a person whom nineteenth-century society doesn't trust with much of anything – except, of course, keeping quiet and looking pretty. When Charlotte boards the Seahawk, however, she must start making her own choices. Learning to think and act for herself becomes a significant part of Charlotte's maturation – and also plays a role in why Charlotte decides, in the end, to not return to a society that doesn't trust her to make her own choices.
Not everything can be a choice. Sometimes we have to do things that we'd rather not do.
It's not so much the actual choice that is important, as it is the opportunity to make that choice.