Although Shakespeare's play is named after him, Julius Caesar is not the play's protagonist. He is certainly a very important character--and a real figure in history--but he is not Shakespeare's central character in the play. Although his ghost appears briefly later, Caesar's role in the play effectively ends in Act III with his assassination.
In addition, the protagonist is the character who earns sympathy and, sometimes, admiration. Caesar's murder is certainly cruel and painful, which perhaps earns him some sympathy, but he is not developed as a very sympathetic character. He is cold, arrogant and self-centered. He is very vain and easily flattered. He will not tolerate any political dissent in Rome. Also, Shakespeare implies that Caesar misuses his power in some respects.
Shakespeare most likely named his play after Julius Caesar, not because he is the protagonist, but because he and his assassination were so well known to Shakespeare's audience.
I think we can assume that Mark Antony or the Triumvirate as the protagonists as Mark Antony earns a lot admiration at the funeral oratiion of Caesar and we can get sympathy on Antony's words at the marketplace where he sees Caesar's dead body.