Historically, "the Crusades" were a series of military expeditions initiated by the Catholic forces of Europe against Islamist governance in the Middle East, and take control of Jerusalem and other "holy sites" in the Middle East. The Crusades began in the eleventh century A.D. and continued for another six centuries.
They were a bloody and brutal affair and included many aspects of what later came to be called fanaticism and colonization. While, initially, Muslims tended to obey conventions of war rigorously, and despite constant atrocity by Europeans (including in particular the horrific taking of Jerusalem in the First Crusade), held to a prohibition against harming civilians and noncombatants. When retaking Jerusalem, no retributions or revenges of any kind were committed, and a strict point was made of respect for the Christian faith. Despite these good examples however, atrocities continued, and over time the behavior of the Muslims tended to get worse, and of Christians better - possibly either the result of regression towards the mean or simply the fact that in the early days, it was elite educated Muslims and poorer "adventuring" Christians that tended to command. Over time, the Crusader States became established, and more respectable Europeans arrived, while Muslims became more desperate to expel them. This was eventually done by the time of the Ottoman Empire.
The term "Crusade" is based on the word "cross", whose symbol was worn as a badge or heraldic symbol by those who participated. The use of the term Crusade literally translates to "War of the Cross", of Christianity versus Islam. It is also worth noting that the historical Crusades, after the first, were dismal failures. Comparisons to modern military "quagmires" are somewhat appropriate. Due to the above history, Muslims generally understand the term "Crusade" to mean religiously-motivated genocide and colonization.
George Walker Bush initially referred to his War on Terrorism as a "Crusade" and code-named the initial plan to invade Afghanistan "Operation Infinite Justice." These linguistic usages offended Muslims, who regard "infinite justice" as the province of Allah, so the code name for the war in Afghanistan was later changed to "Operation Enduring Freedom."
Compare the Arabic "jihad", meaning (roughly) "holy struggle", "struggle" or "striving", a religious duty in Islam that can be both personal and communal. Westerners often take this term to mean "holy war", and the term is used as such by some militant factions or splinter groups within Islam. The struggle to expel Europeans in the Crusades were in fact referred to as jihads in many cases.