Since Marcus Junius Brutus was a teen, his uncle, Julius Caesar, had been carrying on an affair with his mother, Servilia. Added to this relationship, Caesar considered Brutus a beloved nephew. Further, while Shakespeare portrays Brutus as noble-minded, the historical records point to Brutus as more politico than appears in the play. For instance, Brutus sided with Pompey the Great against Caesar in the civil war in spite of the fact that Pompey had killed his father.
So, when the shocked Caesar asks, "Et tu, Brute?" [Latin for "And you, Brutus?] he expresses surprise that his beloved nephew would stab him, knowing also that his mother loves Caesar. He should not, however, have been surprised at any lack of loyalty on the part of Brutus since he previously sided against him with Pompey. On the other hand, Shakespeare has been known to have changed historical fact in other history plays, so in this play Brutus's relationship with Pompey may not factor into the motive for killing Caesar.
In William Shakespeare’s play Julius Caesar, the character of Marcus Brutus is alone among those conspiring against the increasingly dictatorial Caesar in acting reluctantly and only because he believed the assassination was vital to the survival of the Roman republic. While Cassius, Trebonius, Ligarius and the other members of the Senate involved in the conspiracy act out of less altruistic motives, Brutus holds firmly to the belief that Caesar’s autocratic ambitions bode ill for the quasi-democratic nature of the existing political system. In this, he is entirely sympathetic to the notion of eliminating his old friend and colleague. During the conversation when Cassius is attempting to recruit him for the deed, Brutus concedes that public support for the demagogic leader is reaching alarming proportions:
It is Brutus’ honor and general sense of loyalty – traits known by Caesar – that makes him an unlikely coconspirator. It is in this context that, as the assassins close in for the kill, the mortally wounded Caesar, recognizing the participation in his assassination of one so honorable, utters the classic line, “Et tu, Brute! Then fall, Caesar.” It is Brutus’ involvement in the scheme to murder him that leads the fallen, dying leader to lament the treachery while accepting its apparent inevitability.