Are you worried about fraying before or after you apply the fusible? In other words, will you apply the fusible before you wash the flannel?
I wash and dry flannel twice without sewing around the edges. There is some fraying on the cut ends, but it's not a problem for the selvage ends. When I take the flannel out of the washer, I clip the frays off, then put it in the dryer. After the second wash/dry, I cut the width of the fabric to get a straight edge. So far I haven't used fusible on flannel and it seems to sew up and stay together without fusible. However, I usually quilt relatively closely, and that helps keep seams together.