Well, I can see that we are probably not going to agree on this issue. The standards that I apply are standards based upon my belief system. Certainly, Western civilization has changed since the Middle Ages, but Christian principles haven't. To crowd Jews into a synagogue and burn it down because they chose not to convert to Christianity is wrong. To slaughter Orthodox Christians because their form of worship was different (and not to a great degree), is wrong. To rape Islamic women and justify it by stating that they are infidels is wrong. It doesn't matter whether or not it was common practice. The standards of their belief system (Christianity) clearly spell out that this type of behavior is wrong, regardless of the justness of your cause. And THIS is what people "remember" when we begin to talk to them about what we believe. If Christianity is so good and virtuous, then how could people have done these things in the name of Jesus Christ, on a Crusade for Him? Well, according to the teachings of Christianity, they shouldn't have! Unfortunately, but not suprisingly, Islam allows for terrible deeds to be done in the name of religion. I still believe that those deeds are terrible and wrong. But, their belief system does not tell them not to do such things. Mines does, and so did the Crusaders'.
Fighting a war, liberating the Holy land, even killing the enemy, these things are not necessarily wrong, although they are unpleasant. They are quite noble when done for the right reasons, and carried out in the right ways. Now of course, ugly things happen during war, and not all of it is justified. Even some things done under orders are morally wrong. I find it suprising that in a group where conservative principles are valued, the belief that moral wrong IS wrong regardless of the generation or common practices of a people should be a novel concept.
Also, I don't think that you're hearing everything that I have to say. The apology was not directed solely at Muslims. It was geared equally toward Jews and Eastern Orthodox Christians. Unfortunately, the press did not emphasize this as much. But I worked with the walk both in Turkey and Israel, and was able to share it with people of all three faiths. Contrary to your belief, I do not believe that it encouraged jihad (which was already in full swing by the time the Walk began. And I know this, because I was in the thick of it going to grad school in Israel at the time). I think that those who were going to respond to it did, and those who were bent on jihad were already inclined toward extremism, and our efforts made no impression on them except maybe to maintain an already seething disdain for anything Western. In short, I don't believe that the bad got worse, or that they were emboldened by our statement. The kinds of things that encourages radical Islam are, for example, when countries back out (ie Spain) out of fear of terrorist reprisal, or cowtow and change their laws in order to avoid terrorist threats (as the terrorists are trying to force in France). Another example is when the Israelis pulled out of Southern Lebanon in 2000, their enemy then getting the impression that they had worn down their resistance. This is the kind of thing that emboldens Islam. Simply sharing a truth of Christianity does not. Humility doesn't imply weakness, and those who perceived the apology as weakness already held that view of the West. But I know for sure that there were countless others who were sincerely moved, some to tears, and who even then began to understand something of the spirit of Christianity, once they were able to remove what they had alway understood it to be as a result of what they'd learned of the Crusades.
Also, I know that Islamic civ collapsed years ago. I believe that I may have been using the term simply to refer to the Islamic world, which though fragmented, still has a unified ethos worldwide. During the period of Islamic civilization, however, there were many great inventions and discoveries and great centers of learning which developed. The Islamic world actually did contribute to the continuing development of the Western world. They just got stuck in the Middle Ages, and are still unwilling to leave it. They're still looking back to the days of their "golden age". While I disagree wholesale with the religion, the radicalism it spawns, and the worldwide manipulation that has developed as a result of it, I will not deny them their heritage. Islamic civilization has a very rich history, and the information that it was able to transmit to the west (even knowledge gained from farther east) was of great benefit. And, we often received it once it had been synthesized through an Islamiic filter. Scholasticism and the concept of merging faith and reason were blatantly Islamic, learned by Western medieval thinkers in Islanic universities like those of Cordoba.