God knows that Cain understands the proper relationship between brothers. So, He ignores the question in the previous verse. He asks “What hast thou done?” He knows what Cain did. But, the notion of taking another human’s life was such an awful thing, God wanted Cain to realize that this was something far worse, as far as consequences, than most sins. While all sin keeps us away from God, the notion of taking another human’s life is much more heinous than most, because this is a person who is in the very image of God.
This is why God speaks of “the voice of Abel’s blood” crying out from the ground. The same picturesque language is used in Revelation 6:9-10, to show the cries of many martyrs, who have suffered terribly throughout history.
People all the way back to Abel have suffered for the testimony of God’s grace and mercy. Countless numbers of people have suffered at the hands of those who would rather get to Heaven by their own good works, when in fact nobody can work their way to Heaven. It is “not of works, lest any man should boast.” (Eph. 2:9) God demands an even playing field, for our benefit. He doesn’t want it to be any harder for one person than for another to receive His gift of salvation. It is free to all who receive. It may take a long time. But, God will repay all who have suffered for their faith in him, through His perfect judgment.