The problem is the disconnect between muslims.
In my experience, there are muslims (mostly western born, raised, educated) who believe that "Islam is a religion of peace and tolerance."
There are also muslims (mostly born, raised, educated in muslim countries) who believe that "Islam is a religion of peace and tolerance."
One might think "whats the difference?".
Well, for the 'westernised' muslims, 'peace' and 'tolerance' mean pretty much what any other english speaker would think they mean. For the 'muslim' muslims 'peace' means 'because you are not struggling against the will of God you are at peace' and 'tolerance' means 'tolerate other muslims'.
Theres a massive schism in Islam, its as if there are two completely different religions which occupy the same 'space' but which are completely opposite in many ways.