To say Islam is intolerant is to generally claim that Muslims are intolerant.
Absolutely not. Organized religions, such as Islam and Christianity (or rather, Catholicism, Shia etc.), are themselves power structures perpetuating values.
Criticizing a religion is no more a criticism of the individual believers than calling a national government (like the Russian one maybe) evil is equivalent to claiming all who share that nationality are evil.
I would also strongly dispute your claims regarding the history of islam, but don't have time to take that discussion right now. My statements regarding islam as a religion in the current day I will stand by however.