The protagonist is the central character in a story. The writer intends for the audience to identify with and feel sympathy for his or her protagonist. In this tragedy, Brutus is Shakespeare's protagonist, even though the play bears Julius Caesar's name.
Brutus is the play's central character. It is his story that unfolds from the beginning of Act I through the conclusion of Act V. Shakespeare develops Brutus as an honorable man who struggles with a terrible conflict: to remain loyal to his good friend or to his beloved country. Brutus tries hard to do what he perceives to be right.
Brutus becomes even more sympathetic when the audience realizes that Cassius is not only encouraging Brutus to join the conspiracy to murder Caesar, but also tricking him. Cassius deceives Brutus by making him believe the citizens of Rome are begging him to protect their freedom. When Brutus does join the conspiracy, he does so believing that their cause is noble. After Caesar's assassination, when he disapproves of actions taken by Cassius, he reminds Cassius in a very emotional speech why they killed Caesar. He must believe that Caesar's death was for the good of Rome.
At the play's end, a defeated Brutus chooses to die with honor. Shakespeare reminds the audience that his protagonist was an exceptional man, worthy of admiration and sympathy. Antony says, "This was the noblest Roman of them all." Furthermore, Antony adds that Nature herself should tell the world, "This was a man."
I've always seen Brutus the protagonist--the prominent good guy, "the noblest" by Antony's final speech.
But let's look at that speech again. Antony says "the noblest Roman of them all," not the noblest man; he juxtaposes absolute value "great Caesar" to the stipulated "general-honest" and "common good" rather than honest or good; he undercuts "to all" generosity with "only he," "He only," and "one of them"; with "His life was gentle" and "save only he," he contradicts the murder in "made"; he calls the body "This," not "He"; he calls him unstable, not in-balance or proportioned but "elements so mix'd in him"; and with "This was a man!" he has Nature point to a dead body, the suicide. Antony never uses Brutus's name and mocks Brutus's morality--the conspirators all had reason to kill--Brutus had none; in fact, Brutus uses faulty reasoning, applying a general condition of human nature to the specific person--that gained power may corrupt Caesar--to abstract a cause for his foregone decision to kill Caesar: "It must be by his death."
So Cassius seems more of the protagonist. Cassius plans; Brutus frustrates; also, Cassius speaks first about the scheme ("proto"+"agonist"); he competes ("agon"), develops respect for the gods/omens, dies for love, and wears the laurel wreath.
Problem is, Brutus tries to be a good guy antagonist--he wants to write a script of murder and betrayal that rights the plot of assassins and liars.