If you read the question carefully I ask Intolerance in "Muslims" and not Islam. Islam is one of the most tolerant religions of all, but one thing that's oxymoron is intolerance in Muslim fanatics.
I have had a hard time dealing with Muslim clergies and orthodoxy big time. There is aggression and intolerance in them which is hard to counter. I believe this can be one of the seeds of all the ills of Muslim brotherhood that we witness at various places.
What is the reason it exists? Why are some of us so intolerant? Is their any historical or contemporary event/events responsible for it?