To get past the standard half-truths and distortions about Islamic tolerance and victimhood, it's necessary to read "the rest of the story."
Robert Spencer forcibly analyzes and demolishes common myths in three invaluable books: Onward Muslim Soldiers: How Jihad Still Threatens America and the West (2003), The Politically Incorrect Guide to Islam (and the Crusades) (2005) and Religion of Peace? Why Christianity Is and Islam Isn't (2007).
Despite their own theological errors, Norman Geisler and Abdul Saleeb still provide a valuable doctrinal biblical analysis of Islamic theology in Answering Islam: The Crescent in the Light of the Cross (1993). A less careful but more readable book in the same vein is Robert Morey's Islamic Invasion: Confronting the World's Fastest Growing Religion (2001).
Harvard professor Samuel Huntington, in The Clash of Civilizations and the Remaking of World Order (1996), generally analyzes how the sources of conflict in the post-Cold War era now originate from civilizations (groupings of nations with similar basic culture). Here he provides highly specific empirical evidence that supports his provocative statement that Islamic civilization has "bloody borders."
In two key books, Bat Ye'or provides the basic evidence about Islam's history of intolerance that most Western academics continue to ignore: The Decline of Eastern Christianity Under Islam: From Jihad to Dhimmitude (1996) and The Dhimmi: Jews and Christianity Under Islam (1985). Of a similar scholarly nature, but focusing on the history of jihad in particular, is Andrew Bostom's The Legacy of Jihad: Islamic Holy War and the Fate of Non-Muslims (2005).
Israeli historian Efraim Karsh documents in Islamic Imperialism: A History that Islamic terrorism and wars are historically rooted in the religion's intrinsic expansionary drive. And one of the leading academic authorities on the Islamic world, Bernard Lewis, explains (in What Went Wrong?) why Islamic civilization went into a long decline after having been more developed than the West for centuries.
Instead of relying on how other people summarize the Koran's teachings, some readers may wish to read Islam's central religious text for themselves. For general, non-Muslim readers, perhaps the best English translation of the Koran is by N.J. Dawood (1956). However, Muslims respect Maulana Muhammad Ali's translation (originally published in 1917) more, which also numbers the sura and verse divisions much better. The Koran is also available online.