I haven't read his books. I've only read a few of his essays and articles, and some things about him. He's a smart man, a courageous man, a man of the world.
I doubt many of us equate Islam with Christianity. You may.
I don't.
I'm sure Rushdie doesn't. After all, he's chosen to live in the West. I also doubt that he thinks religion is responsible for all of man's failures, weaknesses and sins...or that a secular society is proof against them.
But he's found elements of all religions that he doesn't like and it isn't difficult to guess what they are; certainty in an uncertain world based on "scripture", intolerance of alternate views - especially those which question "scripture, self-righteousness, small-mindedness, fear of sexuality.