I think you are conflating the left's support for minority groups who are demonized and targeted by society for support of the tenets of their respective religions. After 9/11, Muslims were a significant target of hatred and violence. The left, which again is not a monolithic entity, doesn't support islam anymore than it supports judaism or any other religion, it supports people who happen to follow that religion. It's based around humanist tendencies, which the right often doesn't understand. You can hate aspects of a religion while also being against any dehumanization and hatred against people who follow said religion.
Like the other 2 major Abrahamic religions, Islam has some good and some bad tenets. At least in the US, there are some extremely conservative muslims and some - perhaps shockingly - liberal muslims. Being that they are such a small percentage of the US population, there is a lot of misunderstanding and stereotyping of people who follow Islam.