We've got to say, it's a pretty straightforward, common choice to name your book after its main character. Charles Dickens did it with David Copperfield. Charlotte Brontë did it with Jane Eyre. Rick Riordan did it with Percy Jackson and the Olympians (though Mr. Riordan gets extra credit for the exciting Greek mythology reference, there). Anyway, what we are saying is that by titling Kim after, well, Kim, Kipling is not alone.
But there is a difference between Kim and other, earlier nineteenth-century novels like, say, David Copperfield. Even though we may have no clue who this guy David Copperfield is, we can guess a few things from the name. First off, with a name like David, he's probably a guy. There could be a twist, but we are still probably supposed to assume that David is a boy. What's more, David has a supremely English last name: Copperfield. Again, we can't say for sure that he is living in an English-speaking place without reading the book, but it's a pretty fair guess.
Of course, "boy" and "probably English" are not much to go on in guessing the plot of David Copperfield. But at least it's something, right? Whereas Kim, well, that could be anything. In fact, in this day and age, when Kim is usually short for Kimberly, we would probably assume incorrectly that Kim is about a girl. And without a last name, we really can't guess anything about who this person is or where he is from.
So Kipling may name Kim after his main character, but he does it with a twist. The ambiguity of the name Kim makes this title more mysterious than anything else. The character of Kim is a chameleon, adapting to each unique situation he finds himself in, so it makes sense that his name—and the title of the book—is as vague and obscure as he is.