This is a question that has been asked millions of times. And yet, there is still no definitive answer even from the hundreds of historians who spent countless hours poring over the documents and artifacts left by both the Crusaders and the Jihadists.
On the one hand, there is the argument that the Crusades were necessary in order to repel the threat of the advancing Muslim invaders. Without the countless knights and ordinary folks taking up arms to defend Christianity, it is entirely possible that the whole Europe would have fallen to the swords of the enemies.
On the other hand, there are historians that cite records of Crusaders pillaging, murdering, raping, and doing all evil things. For them, the real reason for the Crusades is the insatiable greed of the Crusaders and the people backing them.
If there is one thing that they agree, it is that the Crusades were launched against Muslims. As to why, that is the hardest part to answer.
For more information, you could check out the following links:
http://www.history.com/topics/crusades
http://www.newadvent.org/cathen/04543c.htm
http://history-world.org/crusades.htm