We know Frodo is our protagonist because, when he completes his quest (even if it is kind of accidental), he gets a song sung about him in the novel itself: "For I will sing to you of Frodo of the Nine Fingers and the Ring of Doom" (6.4.50). If you've done something important enough that people are singing about you in your own novel, you're probably the protagonist.
Frodo deserves a lot of the credit for the Ring quest, because he's the one who carries the Ring from Rivendell right to the edge of Sammath Naur. But Sam is the one who gets Frodo deep into Mordor in the first place. As Frodo grows weaker and less able to protect himself, Sam has to step up and support him as best he can. In a lot of ways, Frodo and Sam are two halves of the same coin: Frodo is the leader, Sam the follower. Frodo loses his strength, so Sam grows tougher to support him. And when Frodo must leave Middle-earth to heal from his quest injuries, Sam stays on to continue Frodo's legacy of good deeds at Bag End, in the Shire.
The whole book is called The Return of the King, and Aragorn's the king. Need we say more? Of course he's a protagonist of the novel. Aragorn's return to Gondor, accompanied by the armies of the Dead and by his faithful Dúnedain, is the essential secondary plot of the whole Lord of the Rings story. After all, it's not enough just to destroy Sauron (which is what the Ring Quest is about). Tolkien also needs someone strong to rebuild Middle-earth after Sauron's horrible influence is gone. And that someone is Aragorn: he is the character with the lineage and natural abilities to restore Gondor and all of its lands to their former glory.