I just saw Mr. Harris on CSpan, and feel that he is not entirely fair in his views on Islam. This is not his fault, he is evaluating Islam on the basis of what Muslims say about it. So, it is easy to find fault with it.
Modern Muslims divide the Koran into two sets of verses, the sword verses, and the verses of reconciliation. It is widely held that the sword verses made the verses of reconciliation and peace obsolete.
Islam has a long history. It started about the same time that Charlemagne ordered the execution of 4600 Chieftains for the crime of being pagans. There are more verses in the Koran commanding religious tolerance than there are in the Old and New Testament combined.
During the first two or three hundred years of its existence, Islam was far more tolerant of other religions than Christianity. Minority Christians and Jews were known to dance in the streets in joy when they were liberated from Orthodox Christian majority rule by conquering Muslims.
Large communities of these minority religions lived at peace in Islam up until the founding of Israel, but back to that later.
Intolerance began to grow in Islam as the Muslims in Europe were pushed back out, followed by the Crusades, and finally the conquest of most of Islam by Turks and Mongols from the Steppes of Asia.
These influences worked to build hostility towards other religions through the Crusades, and increase the emphasis on violence due to the Mongol and Turkish influence. For a brief period a Mongol leader who converted to Buddhism persecuted Mongols in Central Asia, which shows the basic Mongol approach to these matters.
It can be said that Muslims today largely follow the Sharia of Genghis Khan, not the Sharia of Mohammed and that they have indeed picked those passages which were most pleasing to Mongol conquerors out of the Koran and Hadith.
The creation of Israel convinved Muslims that they had to fear religious minorities as fifth columns within Islam which the evil colonial powers of Europe would use to overthrow their states, a sickness of paranoid fear and anger has swept through Islam, making modern Islam quite contemptible, and producing hysterical oppression of religious minorities.
I only wish to make the point that it was not always this way. At one time it was the most tolerant of all the Judeo Christian Islamic family of religions.