Brutus is the hero of the play, Antony is the villain (or rather, antagonist). Caesar is neither, but his death is the catalyst for the play. If the play were actually about Caesar, he would not have expired in the middle of the play. You're right that Shakespeare does not portray Shakespeare as an out right villain. Much of the bad stuff we hear about him from Cassius seems to be based on envy rather than fact. When Caesar decides to go to meet with the Senate in spite of his wife's warnings, he says
Cowards die many times before their deaths;
The valiant never taste of death but once.
Of all the wonders that I yet have heard,
It seems to me most strange that men should fear;
Seeing that death, a necessary end,
Will come when it will come.
Pretty heroic stuff, in ringing iambic pentameter.
Should have read "does not portray Caesar"