I read The Heart of Islam by Seyyed Hossein Nasr. This book has cleared up some of my confusion. I know that he does not speak for all Muslims, but what he says makes sense from the point of view of Muhammad being an enlightened soul. Nasr says that the Quran states that the only justified war is a defensive war, and that there should be no compulsion in religion. He says that when people want to fight an aggressive war, they use whatever ideology will appear to give legitimacy to their efforts, be it religious or political.
If this is the case, it means that when Muslims have fought aggressive wars or tried to compel people to convert to Islam, they are going against the Quran. Nasr says that the Jewish and Hindu scriptures have as much advocacy of war as the Islamic scriptures, and that we in the west single out Islam due to prejudice.
I can see now that Muhammad may have had a revealed message that was later misinterpreted. Nasr says that Islam is a religion of peace. Now I can feel more confident that all religions are paths to God, and their founders were enlightened souls.
Salaam, Shalom, Pax vobiscum, Shanti