The truth is that these acts of terrorism were not based on the Qur'an but on anger and a desire for vengeance and violence. These actions have nothing in common with the teachings of the Qur'an or of the Prophet Muhammad. Compassion and mercy are a central tenet of Islam, and these two attributes are the first two attributed to God. In fact, they are mentioned at least 192 times in the Qur'an in reference to God's mercy and compassion in comparison to only 15 mentions of God's wrath. Terrorists and extremists can find very small portions of the Qur'an to justify their violent acts against people of other faiths all the while ignoring the vast majority of the Qur'an that preaches non-violence and tolerance for those of other religions. Many of those passages are then taken out of context and misused, giving the rest of the world a false view of Islam that has almost nothing in common with how actual Muslims conduct themselves. This is not specific or unique to Islam, Christianity has had this same problem for centuries. Particular passages of the Bible, taken out of context have been used to justify horrendous acts, such as slavery and the torture of those of other faiths.
Across the Qur'an as a whole a theme that is constantly repeated is the tolerance for other religions. In fact, there are many passages in which it is said that Jews and Christians can also find salvation if they are rightly guided and perform good deeds. The Qur'an teaches respect for the Old Testament and for the Gospels and in the earlier days of Islam, Muslim conquerors were unique in that they never imposed the Islamic faith on the people of the nations that they conquered in war. In fact, as historically Muslims regard Ishmael as their ancestor and Isaac as the ancestor of the Christians and Jews, there is a common theme in the Qur'an of regarding Christians and Jews as brothers to the Muslims. They are all united by the book, “Brothers of the Book”. While many non-Islamic traditions persist and the petty prejudices of scholars and culture can interfere, purely by the Qur'an and the actual teachings of Islam, there should not be any problem between Muslims and people of other faiths.
Islam is strictly opposed to evangelizing, to forcing conversion from other people. The Qur'an clearly states that in religion there must be no compulsion. In his day the Prophet Muhammad protected minorities of other faiths. The Christians and Jews were taxed according to law, but this was to put them on equal footing with Muslims that, as a central part of their faith, payed a percentage of their earnings to support the disadvantaged and the poor. An outstanding historical example of Muslim tolerance for other religions was the situation in the portion of Spain that belonged to the moors. For at least 750 years Muslims, Christians and Jews lived in the same place without violence or oppression, each free to worship in the way they thought convenient. It was only in 1492, when Spain was retaken by the Christians that those unwilling to convert to Christianity were killed or deported in the Inquisition.
A concept that is largely misunderstood by non-Muslims is the concept of Jihad, of holy war. The concept of Muslims engaging in a war in the name of Allah, killing people of other faiths has nothing in common with the rulings in the Qur'an, much like the Crusades and the Inquisition were not an accurate representation of the teachings of Jesus in the Gospels. It would be hard to find a monotheistic religion that actively defends violent behavior. Islam only allows war in self defense and never as the aggressor. The Qur'an clearly states that fighting should only be used to defend oneself and that God is not on the side of aggressors. In the context of the historical circumstances of the Prophet Muhammad's time and the intense violence against Muslims of that time, the wars that Islam engaged in its early days make sense. However, much like the violence of many Popes and European rulers of the Christian faith, the holy wars of some of the Muslim caliphates were never a true representation of the teachings of the religion.
One key aspect of the Qur'an that is very similar to Christianity is the exhortation to love your enemy. Many so called Muslims today would do well to remember this. People of other faiths would also do well to understand the difference between fundamental, radical Islam and Muslims all over the world living their lives in peace.