Although Eustace, Caspian, and Lucy share the stage in The Voyage of the Dawn Treader, Eustace is in some ways the most important protagonist. After all, he is the only one who goes through significant character changes over the course of the novel. When we are introduced to Eustace in the first chapter, the narrator goes out of his way to make it clear that Eustace is totally obnoxious, which makes us suspect that the adventures in the novel are going to reform him. Eustace is most clearly the protagonist in the adventure on Dragon Island: he's the one who gets transformed into a dragon, and the narrative follows his thoughts and feelings for three chapters as he goes from a boy to a monster and back to a boy (although he's a very different boy in the end!).
As the current reigning monarch of Narnia, King Caspian often takes center stage in The Voyage of the Dawn Treader. He clearly has the last word on most decisions regarding the ship, its crew, and its adventures – except for when Aslan steps in and overrules him. Caspian takes the lead in the Lone Islands when his friends are captured by slavers, and goes so far as to overthrow the local government and establish a new one. Caspian is also the only character in the book with a love interest – Ramandu's daughter – though his relationship with her is only described in passing.
As in several of the Narnia books, Lucy Pevensie is the most sympathetic and faultless of the protagonists. She is compassionate and forgiving, even when dealing with her irritating cousin Eustace, and the narrator often explores her consciousness when trying to express the beauty and power of Narnia. In some ways, Lucy seems like a "holdover" protagonist from the first two Narnia chronicles, The Lion, the Witch, and the Wardrobe and Prince Caspian. As in those books, C.S. Lewis's narrator is extremely comfortable exploring her thoughts. Lucy is most clearly the protagonist in The Voyage of the Dawn Treader in the adventure with the Dufflepuds, where she must brave the house of a mysterious magician and search through his books for a counter-spell.