Flannels are great for battings in (quilts for hotter climates) baby quilts that are going to be washed a lot. I use flannel for wheelchair quilts batting. For batting in preemie quilts, bibs, and for purses a lot of time. I use flannel in all my raggy quilts between the layers of cottons or denim.
It's better to zigzag each end and wash and dry in dryer (a couple of times) to shrink it if you are going to use it in anything but the raggy quilts.
All flannel is not the same quality, same as quilting fabrics. Check the weave and weight of it before buying. If it's not a good heavy quality you get more fraying and pilling. I've been there done that.