Yes, at first, he seems completely wrong but his acting absolutely made him perfect for the role in much the same way that Glenn Close was not looks-wise the right woman for Fatal Attraction but she sold it so you can't imagine anyone else in that role.

I have to agree. He as a person is not that attractive. But the way he played this role - his mannerisms, his smirks, his eye rolls, his coyness, etc. were very, very seductive even for us as viewers.

I agree.
I also thought this about him as Mr. Hyde in Mary Reilly.

There are many who felt this way, me included! I think there are more posts like this on this thread. Malkovich isn't attractive, per se, but the way he played this character made me want to sleep with him!
What a waste. Oh, the humanity!