Brutus is for what is good for Rome. Whatever we may say or read into his decisions with our hindsight, he does what he believes to be honorable and noble where Rome is concerned. Cassius targets Brutus because of Brutus' reputation. Without Brutus, Cassius knows that the conspiracy will have a snowball's chance in Hades at getting out on the other side with few, if any, scars. Cassius is manipulative, conniving, and greedy. Caesar himself recognized this by saying that Cassius had a "lean and hungry look"--meaning that Cassius is not to be trusted by anyone.
I think it may be more complicated than that explanation-Brutus is a patriot and Cassius wants it all. Brutus is weaker when it comes down to decision making. He makes some decisions that destroy the conspiracy, for example, letting Mark Antony speak at Caesar's funeral. Brutus does betray Caesar and chooses to stab him, whether it be for the good of Rome or not, illustrating his ability to deceive.Then Brutus makes other poor decisions illustrating either weakness or naivete when it comes to Mark Antony. Cassius has one goal-to remove Caesar-he is successful at that goal.
Brutus is a patriot. He wants to do what is right for Rome, always. Cassius is a greedy, jealous, and power-hungry man. He wants to kill Caesar because he is jealous of Caesar's glory and power, and wants it for himself. Unfortunately, he understands Brutus better than Brutus understand him - that is why is able to so convincingly prove to Brutus that Caesar is dangerous to the republic.