The highest casualty estimate is at 3 million, which for it's time is not that big at all.
I'm not so sure I agree that 3 million is "not big at all," or that death toll is in any way a useful metric for determining the "importance" of a war, but let's leave that aside.
I'll talk about two reasons why the crusades are important; there are many others.
First, they combined the ideas of justice, religion, and warfare in ways that did not exist previously. Violence had previously been sanctioned by religious authority in the Christian tradition, but it had never been in and of itself a holy act. It is important to say that this fusion is not inherent in crusading from its origin, but rather was the creation of the theological discussion which surrounded the crusades. This in turn was an important and formative step in what we know call Just War Theory, specifically through the works of Thomas Aquinas in the thirteenth century. The Second World War, for example, has been called both "the Good War" and "the Last Crusade" because it was a justified battle against an obvious evil.
The second point plays off the first. The 19th century saw the rise of what we call "medievalism" - the anachronistic and idealistic imagining by Romantics as to what the Middle Ages actually was. This appears in literature in the form of a surplus of novels on King Arthur and the Crusades (see Ivanhoe, etc.). It appears in architecture in the form of the neo-gothic style, found in places like the University of Chicago and the cathedral of St. John the Divine in NYC. In popular culture, it appeared in the enthusiasm and the propaganda for the First World War. Moreover, this renewed interest in the crusades coincided with the fall of the Ottoman Empire and the rise of Arab nationalism. Ṣalāḥ ad-Dīn Yūsuf ibn Ayyūb - Saladin - had been pretty much forgotten since the late thirteenth century, but he was rediscovered and became a cultural hero in this period. He was such a symbol of Arab unity and nationalism that Saddam Hussein even had statues of Saladin made, which is moderately ironic since Saladin was a Kurd. This trend continues to the present day, but we run into the 20 year rule so I'll leave it at that.
The crusades remain important because they are still influencing cultural practices and group perceptions 920 years after Urban II's fatal speech at Clermont.
Alexander, Michael. Medievalism: The Middle Ages in Modern England. New Haven: Yale University Press, 2007.
Madden, Thomas F. The New Concise History of the Crusades. 2nd ed. Critical Issues in History. Lanham: Rowman and Littlefield, 2006. Contains a lot of discussion on the modern importance of the crusades post-9/11. I don't agree with most of it, but it's an interesting read.
Reichberg, Gregory M., Henrik Syse, and Endre Begby, eds. The Ethics of War: Classic and Contemporary Readings. 1st ed. Malden: Wiley-Blackwell, 2006.
Remember that the world's population was under 1 billion until the 19th century. Adjusted for inflation you are looking at something like 21 million dead today. Not that 3 million should be considered "not that big at all" past, present or future...
Why do you say 3 million deaths isn't big for its time?