The title of the play as The Tragedy of Marcus Brutus would make sense if one reads the play outside its historical context. Critics, scholars, and readers often debate the question of who the protagonist of the play actually is. Even though the play is named after Julius Caesar, the development of the story and its characterization do not suggest that Caesar is the play's protagonist. Brutus goes through major internal conflicts throughout the play, and thus seems more suitable to be named the protagonist of the play.
But the play is a re-vision of the actual conspiracy against Julius Caesar and an allusion to England's own fear at the time about the successor to the throne. So the play has to keep the title The Tragedy of Julius Caesar to maintain the parameters of the allusion.