With the popularity of atheist windbags lately, we've all heard how bad the Crusades were, and how awful Christians are for having such an awful incident on their record. The first part is true—the Crusades were awful, and there's really no way they can be justified on any level. However, to attribute the sentiments leading to the Crusades to Christian sentiment is to fundamentally misunderstand the nature of the European attacks on the Middle East.
The First Crusade (1096-1099) was almost purely political. Sure, there was some religious rhetoric thrown in to encourage knights to sign up, as well as an offer of indulgences for past sins, but mostly Pope Urban II called the First Crusade in order to keep Seljuq Turks out of the Christian Byzantine Empire. The armies who took up the call ended up reclaiming Jerusalem from the Muslims in 1099, and a tradition was born.
Medieval Europeans were perennially confused about the relationship of religion and the state. The two were inseperable to them, so that anything protected or encouraged by the Church was necessarily protected and encouraged by the State, and vice versa. This didn't mean the two were never at odds, but it was in a political and personal fashion rather than doctrinally or philosophically based.
Popes attempting to raise armies to send to the East cited all kinds of reasons why knights should leave their estates and go fight the heathen. Partly, they emphasized the knights' love of combat, their lust for glory, and their desire for wealth and power. Indeed, with all the small states set up by Europeans in the Middle East during the course of the Crusades, there was always plenty of opportunity for all those things.
But then, as though aware that divine sanction was sometimes the greater motivator, they would throw in forgiveness for sin, the delight of God, a place in heaven, and the favor of the Church as prizes successful or faithful knights could expect. Reading some of the literature from the period gives the impression that only the most pious attitudes were at work, but there was always an underlying politicism to all the spiritual jargon.
As the Crusades continued (the Ninth and last Crusade ended in 1272), things got progressivley more odd and more secular. The monk knights known as Hospitallers and Templars (as well as many other orders) were integral throughout the period, but they often descended into mysticism that focused on the veneration of relics, the idolization of the Holy Land itself, and other un-Christian attitudes.
Probably the main reason the Crusades are so often associated with true Christianity is that they're associated with evangelism and missions, and such violent measures for the spread of a religion are suspect at best, and at worst, blasphemous. The Crusades, however, were not primarily evangelistic ventures, but "holy wars," in the sense that proponents of one religion were fighting those of another; the problem was, the "Christians" in the equation were often Christian only in name, birth, or political affiliation.
If we can get over the desire to defend all those who profess the name of Christ for impure motives, maybe we'll be able eventually to distance ourselves from the horrors of the Crusades. At the same time, enemies of Christ will always be looking for ways to defame His followers, and the best thing we can do is to be aware of the truth ourselves, and have a response ready for those intent on distorting the truth or perpetrating lies.