We spend a lot of time in Lina's head, so that's one easy way to figure out that she's one of the protagonists in this book. But we also begin to identify with her and empathize with her. Like when she's wishing really hard to become a messenger on Assignment Day, we find ourselves thinking, "Man, that must be the awesomest job in the history of jobs! We sure hope she gets it!"
We also get to watch Lina's thinking evolve from only caring about messenger-ing to starting to care about the fate of her city. Since she's committed to helping people and solving the mystery of the Builders' instructions (a.k.a. doing important stuff that is the focus of the book's plot), we're pretty sure that's another sign she's a protagonist.
Tricky stuff alert: we spend less time in Doon's perspective than Lina's, so it might be tempting to cast him in a supporting role instead of labeling him a second protagonist. But it's Doon's commitment to fix stuff in Ember that gets the plot rolling in the first place (such as getting Lina to consider the fact that Ember is actually in trouble and needs real solutions to problems like power outages and food/supply shortages).
And Doon is so driven to fix stuff—and receive recognition for it—that he pairs up with Lina as well as goes on solo quests to look for clues. His motivations are key in moving the plot along, and by the end of the book, he and Lina are so deeply in this together that we couldn't imagine the book without him. Total protagonist fodder, if you catch our drift.