This quote from a post to Aziz Poonawalla's blog is fairly typical for Islamophobes:
"Even a superficial reading will show that your prophet conducted raids and wars of conquest against his neighbors."
Yes, a superficial reading "shows" this, but a careful reading doesn't. Muhammad never fought any wars of conquest, he only fought to defend himself against the attacks of the Meccans and their Allies. Islam's wars of conquest were fought by the Khalifs who succeeded Muhammad. War during Muhammad's time was a violent and nasty business, even more so than it is now. Often Muhammad rose above his time, and performed acts of unprecedented mercy and compassion. Other times he had to take into consideration the realities of war, and do things that no one would do in peace time. Did he always make the right decisions? Probably not, he was a man, not a god. But I know I couldn't have handled the moral challenges of his situation anywhere near as well as he did.
Let's take one story the Islamaphobes like to cite: Muhammad's slaughter of 600 Jewish Arabs. Three tribes of Jewish Arabs lived near Muhammads community, abiding by an agreement created by Muhammad known as the Constitution of Medina. Later, in two separate battles, two of these Jewish tribes each formed a secret alliance with Mecca, which almost enabled the Meccans to completely massacre Muhammad's community. The Constitution of Medina specifically forbid any diplomatic or commercial relations with Mecca, because of Mecca's overt hostility to the Islamic Ummah. These particular alliances, however, are generally considered to have been military in nature, and a genuine threat to the Islamic Community. The standard procedure during this time was to slaughter any captured adult male prisoners of war, and sell the women and children into slavery. Muhammad insisted on a more moderate course. Two of these Jewish Arab tribes were sent into exile, and the third tribe, the Banu Qurayza, was allowed to remain as neighbors.
A few years later, One of these exiled Jewish tribes returned to invade Medina, having formed an alliance with both Mecca and other nearby Arabic tribes. The Banu Qurayza were caught conspiring with this alliance. If this conspiracy had been successful, it would have exposed the Muslim's entire rear flank, and almost certainly have resulted in the slaughter of the entire Medinan community. After this alliance had been defeated, (even though the Muslims were outnumbered more than 3 to 1), the Muslims marched on the Banu Qurayza, who surrendered, and agreed to be judged by Sa'd ibn Mua'dh, a leading man among Aws, a Jewish tribe that converted to Islam. The Banu Qurayza obviously believed that a Jewish convert would judge in their favor, and it is likely that Muhammad, who suggested Sa'd, believed the same. Unfortunately, Sa'd opted for the traditional punishment of killing the men and enslaving the women and children, and the Muslim community overwhelmingly supported this verdict.
At this point, Muhammad said something like "you have spoken rightly", which I think was probably the Arabic equivalent of "OK". Did this express approval or reluctant acquiescence? Muhammad's ideas of peace and justice were radically alien to most people of his time and place, including his followers. I don't think he could afford to overturn the traditional procedure for dealing with prisoners of war once his new ideas had placed his people in danger. He did what he could, but it's hard to expect mercy from people whose life has been threatened. What do you think would happen to Obama if he freed everyone at Guantanamo and several of the ex-prisoners commited a terrorist act? And Obama is dealing with a culture that supposedly accepts the idea that people should not be imprisoned without trial.