I look at it this way... it's all about "world view". They sincerely regard Mohamed (PBUH) as being the final Prophet. They see the Qur'an as the final and most perfect revelation of God. Now, that means that what they do must be viewed in light of what they believe BEFORE we can indeed judge them. Notice, I said "before" we can judge them. Their beliefs offers them what they believe to be unbending divine prerogative. Thus, if God commands anything... it is the commandment of God Almighty in their minds. Any faithful Muslim will not be acting out of malice or hatred, but rather obedience to what he or she believes to be divine will.
Now, with that being said we must also realize that there are various interpretations of the Qur'an just as their are various interpretations of the Bible. Many see the commands given in the Qur'an to be limited to a given time and place. For example, the commandment to slay "infidels" is connected to a certain military conflict between Mohamed's (PBUH) followers and those who had betrayed the treaty, killed peaceful Muslims, were using both treacherous Jews and Christians (Catholics) to assist them. They don't see it as a binding rule for all time, but a command given simply for that specific context. So we have to remember we should not judge Islam as a whole on the more radical extremists and their interpretation of the Qur'an.
I compare the radical Islamists to the radicals in Ireland, Croatia, and early Protestantism that shed much blood as a result of their interpretation of the Bible. For example, it is written...
Romans 13:4
For he is the minister of God to thee for good. But if thou do that which is evil, be afraid; for he beareth not the sword in vain: for he is the minister of God, a revenger to execute wrath upon him that doeth evil.
Many Christians used to believe (and many still do) that this means that a given government is an anointed agent of God to wield the sword to impose justice and/or war. They saw it as wholesale approval from God for their kings and the Popes to wage merciless and blood wars in the name of Jesus. These were indeed the Dark Ages. In a very real sense... Islam is currently experiencing it's Dark Ages. Once this extremism pushes it's agenda so far that entire Muslim nations are in upheaval against them... we might see a glimmer of an Islamic Reformation and a return to a more sane and peaceful way of Islamic life. The Islamic civilization has given us many advancements down through the ages, prior to their sinking into this religious extremism and glorification of war and bloodshed. Wouldn't it be wonderful to see a more tempered and more peaceful Islam in the Middle East one day? I pray that there would be a revival among the Muslim peoples. That many would accept Christ... and that many devout Muslims would be inspired to pick up the banner of peace and true brotherhood so that the senseless killing stops and so that both Muslim and Christian can one day live in relative peace.