This is an understandable question, because Brutus does play a central role, but there are several other points to consider.
First, if you look at things from a historical perspective, not many people know who Brutus is and the only reason why people do know him is because he was one of the chief assassins. The point is that Brutus is a small figure in the larger scheme of things, whereas Caesar is one of the greatest figures of ancient history.
Second, in light of the first point, Shakespeare's play should be entitled after the great historical figure of Julius Caesar.
Finally, the aftermath of Roman history as is shaped by Caesar. His adopted son, Octavius comes to power and begins the Roman Empire.