I always prewash flannel and have made a few rag quilts that still frayed great. Flannel is more "flexible" (stretchy) than regular quilting cotton, it's thicker, and the seams really start to build up with tons of piecing so I don't use a really complicated pattern. I usually just do a D9P. Oh, and your iron and starch can really help keep things straight and flat while working with flannel too!
Depending on your choice of batting, backing, etc., I've never had any of my flannel rag quilts cause problems with my washing machine. I can see how a denim one would be an issue, though. That's one reason I haven't made a denim one -- the weight of it for washing. If you make a smallish flannel one for a child it would be pretty easy to wash. They are really cute in children's prints -- I think you should try one!