Although the prince doesn’t tell us his story directly—the narrator steps in to tell it to us—he’s the one that most of the story happens to, and he’s the one we learn the most about. We know way more about him than we do about the narrator, for example. Plus, the book’s called The Little Prince. (If a book’s named after a character, that’s usually a pretty good sign that character’s the protagonist. Think Emma, David Copperfield, Jane Eyre and so on.)
The prince is our hero. He goes on a quest, has adventures, makes friends, and even finds love (with his rose). All this adds up to protagonist central.