Each and every word of the title is significant and relates, in its own way, to the themes in the book. Yes, every single one of the words. In the study of literature, every word can matter. Think we're crazy? Well, let's take a look.
"The" is a singular article, and that choice is not insignificant. To be "the" true confession means to be the one and only. Pretty appropriate in a book that's all about what it means to be an individual, don't you think? (Just look at us and our fancy literary analytical skills.) Sure, the title of the book could have been "A" True Confession of Charlotte Doyle, but the story Charlotte tells is not just one of many – it's a unique and definitive account all her own.
Sure, Charlotte is a fictional character, but it's important that her tale purports to be true. And that her story is believed! Remember how at the end of the novel her father doesn't believe that any of the events in her journal could have actually happened? That a girl could never have done or seen those kinds of things? Well, this word declares that yes, they sure did happen, and yes, they are very much "true."
To confess means to make known something that is secret or unknown. A confession might relate to a sin, a transgression, or something that simply goes against the rules – just like Charlotte herself. Charlotte's story is itself a kind of confession as she's making known actions, behaviors, thoughts, and ideas that would definitely have gone against the grain of nineteenth-century society.
What, you thought we would skip "of"? Even after we talked about "the"? Yeah, right. Anyhow… "Of" is a preposition indicating possession. To place the word "of" in the title means that this story belongs to Charlotte and no one else. This is actually very relevant stuff because the concept of ownership would've been very important to a nineteenth-century girl – someone who was usually unable to own anything at all.
At last: her name! Charlotte's full name is included in the title because it's important that we're aware that these are her thoughts and observations and not someone else's. The novel is all about Charlotte's journey toward understanding her identity and who she is as an individual. It's also important that the title has both her first name and last name, as including both individuate her (that means to make her into an individual, or to single her out). For more on Charlotte's name see: "Character Clues: Names."