If a Muslim does not follow the commands of Islam found in plain words in the Koran, is he a Muslim or an infidel? 
"The difference is that such individuals and organizations go against the commandments of their holy book"
You wrongly presume that "everybody" takes their "Books" literally. IMO
If a Muslim does not follow the commands of Islam found in plain words in the Koran, is he a Muslim or an infidel?