I suspect that part of the issue is that the Koran covers every part of life and has never been re-written (unlike the bible). It instructs followers what to eat, wear, how to wash and many other things. To those who follow it literally, it is intolerant of non-muslims - there are over 100 verses calling for war with non-believers and instructions about the agonies they should suffer.
Is it an issue to have devout followers in our midst? I am not convinced that liberal values and religious fanaticism mix easily.