It appears that by the end of Shakespeare's Julius Caesar that Brutus has lost sight of his purpose in killing Caesar, may be suffering from remorse while he tries to convince himself of his noble purpose, and that he makes some poor decisions with regard to the battle between his army and Antony's.
The only reason that Brutus agreed to help murder Caesar is that he feared when Caesar became king, he would change, and that it would harm Rome. Brutus puts the good of Rome before his own good. However, he seems to struggle with that decision throughout the play: he loved Caesar almost as much as he loves Rome.
...it is within the anguished workings of Brutus's mind that the issue of tyranny versus freedom is played out.
It is possible that Brutus sees the outcome of Caesar's murder differently than he had imagined. Even while he addresses the people of Rome defending his actions and they initially agree with him, Mark Antony is a powerful speaker who turns the hearts of Rome's citizens against Brutus. Then civil war breaks out. This certainly cannot be what Brutus had hoped for in guaranteeing Rome's welfare.
Brutus and Cassius's agreement to kill Caesar is based on Cassius' lies; they begin to fight—Brutus must know that Cassius does not care for Rome as much as he cares for himself. Brutus continues to insist that his actions were motivated by his love of Rome. Then he hears of his wife, Portia's, suicide. This is another blow.
Even when Cassius suggests that they fight when their army is well-rested, Brutus (for some fateful reason) disagrees, and then attacks Antony's army too soon.
It has been suggested that...Brutus[ is unable] to distinguish his own motives from noble principles.
Brutus is a man who believes that anything done for the good of Rome is a noble cause. He enters into the conspiracy to kill Caesar with earnest and honorable intentions, at least as he sees it. However, Brutus loves Caesar and sacrifices the life of his ruler for his "republican" principles. He murders the leader of Rome, which is dishonorable—it would seem even as Brutus struggles to convince himself that he was justified in his actions. Throughout the horror of the murder, civil war, conflict with his "compatriots," the loss of his wife, and struggles with making the correct decisions, perhaps Brutus is unable to "have his cake and eat it too." One is honorable by acting with honor. It seems impossible to me that dishonorable behavior can be justified by an "honorable" man.
Although Octavius provides a soldier's burial for Brutus, and even Antony praises him by saying that Brutus was a great and honorable man—the essence of a real man—that Brutus cannot believe these things of himself. Antony says of Brutus:
This was the noblest Roman of them all.
All the conspirators, save only he, (75)
Did that they did in envy of great Caesar;
He only, in a general honest thought
And common good to all, made one of them.
His life was gentle, and the elements
So mix'd in him that Nature might stand up (80)
And say to all the world, “This was a man!”
Brutus follows his heart for Rome's sake, but perhaps it would have been better to consult his conscience—his moral compass—as well.