I've made a rag quilt out of flannel as well as several Yellow Brick Road quilts. I had no problem quilting them. Though it would get pretty heavy if you make a king size. Also may not want your block too small with flannel cause of the thicker seams. Oh yea, make sure that you do prewash, flannel shrinks more than regular cotton fabrics.
By the way, welcome to the board from Southern California.