The difference is that such individuals and organizations go against the commandments of their holy book, while Muslims that do not lie, deceive and spread Islam by the bloody sword go against theirs. 
"Help me with your logic here,"
The actions of a few aren't indicative of the whole.
The KKK was/is steeped in God and Christianity and they advocate doing harm to others. Does that mean all Christians are like that? No it doesn't.
Christians denounce other Christians when they perform evil tasks. I'm still waiting for Muslims to denounce the evil their more radical elements perpetrate. Been waiting a while as a matter of fact...
The difference is that such individuals and organizations go against the commandments of their holy book, while Muslims that do not lie, deceive and spread Islam by the bloody sword go against theirs.