Well a bit of both...From what I read, it seemed like he just didn't think that Islam should be questioned and whatever is being preached/taught should be swallowed as a whole...
I am not sure why people keep quoting him if that is who he was! I never bother reading too much into philosophy - doesn't make sense to me though I am doing a PhD (doctorate of philosophy)!! Lolzz...my philosophy is science and I love it when it falls hand in hand with Islam...don't ask me when it doesn't ...
If he taught that everything in Islam should be "swallowed as a whole" then the premise here is that Islam is fundamentally anti-Science which I don't think anyone at the time would have accepted.
I haven't read much on the guy, but I think it is more to do with Muslims themselves going backwards and using him as a scapegoat for their failures.