It's an historic fact that Muhammed gave the order to have all the men in a particular clan of Jews in Medina killed. People who cite the incident often overlook the fact that the clan had a legal agreement with the Muslims in Medina, and that, despite this, the clan conspired with Muhammed's Meccan enemies to connive in his assassination. The assassination attempt failed, and, in a traditional practice of justice in the region, the men were all killed for the perfidy of the clan. The women and children were sold into slavery.

It wasn't very nice. It wasn't based on religious grounds, either. The other Jews in Medina were not affected. Anyone who was thinking about another assassination attempt (there had been several previous ones) probably thought better of it.

Histories of the region and biographies that go back to original sources concur that Muhammed improved the lot of people under his influence, when compared to the situation in Arabia at the time. He displayed and taught moderation, generosity, and honesty. He knocked the slats out from under the revenge blood feud as an expression of civil justice. He also became a political leader, with all the duties such a role entails, including the physical protection of his followers. In the case of Arabia, that meant to wage war.

If the Koran really directs Muslims to convert non-Muslims or kill them, and nothing in between, why are only a relative few participating in the bloodshed? There are millions and millions of Muslims. I suggest you read a little more about Islam, and try to fit it into Arab culture, which is related, but different.