I know that it does seem a bit odd for the Pope to apologize for actions that are centuries old, but Christians are held responsible (as a religious entity) for the actions of those who were said to be acting in "the name of Christianity." To show that this thing still happens, consider this following example. Why is that people were scared that Mel Gibson's Movie (The Passion of the Christ) would cause anti-Semitism? There are Jews today and the Jews in Christ's times were involved in the crucifixion of Jesus of Nazareth. See the connection? Of course, the followers of Jesus do not seek the Jew's apology for their actions (it has been well established that Gentiles, and God Himself, are all equally responsible for Christ's death).
So, the actions of the Fourth Crusade are lamentable. But, there is a bigger travesty. The Crusades were a temporal gluttony of power and violence that shames Christians, or it should, today. There was no reason for the Muslims to have been slaughtered as was the case in the first Crusade. The motives for each Crusade were never anything but temporal and wrong. The Crusades should be a wake-up call for every Christian to follow Jesus more nearly and to follow his teachings more clearly. Christians die for others; they do not kill others.