The first quilt I made was a rag quilt through a class I took and we used flannel. I can't attest to the comfort level as I haven't actually *used* it, but it does have a nice lightweight feel. As others have mentioned, the quilting won't be as visible and you won't get "poofiness".
I would definitely recommend washing and drying on high before using to shrink it. I've only washed the finished quilt once, but didn't have anymore shrinkage because of the pre-washing. Flannel can shrink up quite a bit so make sure you buy enough!