The views of Dr. Kamel Al-Najjar, a Muslim reformist, are worthy of careful study. He makes many points that rarely get appropriately discussed. A sample:
Anyone who studies Islamic history discovers that Islam was tolerant only during the Mecca period, when it was weak. This is the period in which the tolerant verses were revealed, such as the verses... 'You have your religion and I have my religion [Koran 109:6]' and 'Call to the way of your Lord with wisdom and goodly preaching, and reason with them in the best ways [16:125].'...
"Later, the Prophet emigrated to the city of Al-Medina, and the first Koranic sura revealed to him there - the sura of Al-Baqara - starts with a rejection of the other... Later [verses] call to fight anyone who does not convert to Islam: 'And kill them wherever you find them, and drive them out from whence they drove you out [2:191]'... Subsequently, the sura of Al-Tawba was revealed, and the 'verse of the sword': 'So when the sacred months have passed, then slay the idolaters wherever you find them, and take them captive and besiege them and lie in wait for them in every ambush [9:5]'... The 'verse of the sword' and all the [other] warlike verses of the Al-Medina period were revealed later than the verses of the Mecca period, and as the newer verses, they [come to] replace the Mecca verses. According to the religious scholars, the 'verse of the sword' abrogates at least 120 tolerant verses. So where is the tolerant side of Islam?...
"If we put aside the theoretical statements of the Koran and the hadith, and examine the actions of the Prophet and his companions... will we find anything that can be regarded as tolerance and acceptance of the other? The Prophet, after all, drove the Jews out of the Arab peninsula and made raids on the Arab tribes so that they would convert out of fear.
There is much more in this article that needs to be read and studied. I'll need to content myself with only one more quote.
"How can we call for co-existence between religions when the religious scholars of Al-Azhar, Najaf, and Qom say every day that the Bible and the New Testament are falsified, that Christians are polytheists because they worship the Trinity, and that Jews are the descendants of apes and pigs? [When] every Friday, the [Muslim] worshipers call upon Allah to eradicate the Jews. . . .