I haven't made many flannel quilts but on those I did make I used the 1/2 inch seam. I always press my seams to the side because that's what I was told when I was first learning to quilt.

I completed a child size quilt and used a 1/4 inch seams allowance. It worked wonderfully!!

As long as your seams are straight, a 1/4" works fine for me...but, make sure that you are using a little higher number stitch per inch.