He's afraid of what Superman COULD do and doesn't want to wait to find out. I don't think this particular nightmare is what inspires Bruce to act against Supes, and we don't know at which point of the film this sequence will come.
But this nightmare is essentially the manifestation of Bruce's greatest fear, which is being completely powerless to save someone or stop someone from doing something terrible. It all boils down to his parents' death in Crime Alley when he was a boy and completely powerless to stop their killer, Joe Chill. As Batman, he's trained himself to be able to tackle nearly any obstacle or opponent, and to make sure that he would never be powerless to save someone again.
Superman, however, is something that I'm sure he feels powerless against, having seen what he is and what he can do. He recognizes and admits that Superman possesses the power to wipe out the entire human race. In this case, the entire planet is Crime Alley and Superman is Joe Chill.
Great post man. Didn't really think about it from that angle.