First of all, it would be more accurate to say that some parts of the Koran can be interpreted as calls for violence. There are no explicit calls in the Koran that justifies violence against people just because they are non-Muslims. In fact, the Koran does explicitly say that the People of the Book (Christians), Jews, and Al Sabin (usually translated as resigned monotheist, or one who believes in God but not organized religion) shall have no fear nor shall they feel sad as long as the believe in God, the Last Day, and undertake righteous acts. In addition, according to the Islamic Law set up by Muhammad, non-Muslims would be protected as long as they paid a tax for this protection.

Finally, most of the calls for violent acts often cited by people against Islam are from the Hadith. The Hadith is comparable to the oral tradition in Jewish theology, but the methods to verify authentic Hadith from made up things is questionable at best. The Hadith (or sayings of the prophet) was not established and written down until a long time after the prophet died...I believe its between 100 and 200 years. And the only measure to verify its validity was by analyzing the chain of narrators that it came through. So if someone considered a pious Muslims said that this is something Muhammad did or said and he traced this info through a chain of supposedly pious Muslims this piece of hadith would be written into the larger collection of sayings. This haphazard way of selecting valid hadith has led to many questioning any Hadiths validity, and because of this different sects of Islam have entirely different volumes of hadith.