Brutus is indeed in many ways the protagonist of the play, despite its name. He is portrayed as a noble man, a true Roman who wants to put Rome first. He is a complex character but is a rigid idealist whose ideals don't seem to have a strong philosophical background. This leads him to make mistakes. First he allows himself, partially through pride, to be convinced to kill Caesar for the good of Rome, then he allows Antony to live and to speak at the funeral which hurls Rome into turmoil.
Antony is probably the second major character in the play. He is loyal, intelligent, and politically savvy. His speech at the funeral was my first introduction into Shakespeare and remains a favorite to this day. He is the opposite of Brutus in many ways: being flexible he is able to make key decisions quickly and wisely.
Caesar also plays a major role though he dies midway through the play. He is also proud and may have the ambition he is accused of. But, he is also concerned with Rome, and particularly with its average citizens as is evidenced by his will. He loves his wife and is almost willing to stay home for her, but his pride gets the better of him and he goes to his death.
Cassius, the final major player, is jealous and ambitious. He also has a good knowledge of human nature and is able to use that to bring Brutus into his plot to give his plot validity in the eyes of Rome.
Brutus is the tragic hero the play, a good man but inept politican, who ultimately leads the conspirators in assassinating Caesar. Caesar is the dictator of Rome, and at the beginning of the play he returns triumphant from war, causing some to fear he wants more power. Antony is a good friend of Caesar, and ultimately does battle with Brutus after Caesar's death to bring peace back to Rome. Enotes has an excellent site that discusses all of the characters in more detail.