Protagonist
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Character Role Analysis
Qui-Gon Jinn
We have a young Obi-Wan and the Muppet Babies version of Darth Vader in The Phantom Menace, but it's Qui-Gon Jinn who slides into the protagonist spot. This is his show.
He's the character who realizes Nute Gunray is only a puppet whose strings are being pulled by someone scheming in the shadows. And it is his decisions that combat Darth Sidious's various moves, leading to a conflict between the two even if Qui-Gon doesn't realize who Sidious is.
Yet Qui-Gon dies without seeing his goals accomplished. Even if we know his fate going in, we still want to see Qui-Gon succeed, unveil the Sith, and train Anakin to be the Jedi he hopes he will be.
But that's just our take on the movie. Unlike A New Hope, where Luke Skywalker was the obvious protagonist, The Phantom Menace doesn't make its protagonist so clear-cut. Star Wars and film fans have engaged in many an online debate, stating their cases for the protagonist.
Some have touted Obi-Wan as the right choice; some even give the title to Palpatine. Still others have argued that The Phantom Menace has no protagonist and is a film more focused on plot than character. (Source)
While Qui-Gon may be our choice, you'll ultimately have to weigh the evidence and choose for yourself.