I prewash all flannel because it can shrink so much (even quilt shop quality). I paint it afterwards with a solution of Sta-Flo starch and water, toss in the dryer, and then steam iron to restore body and give it some stiffness.
I once had a class with Harriet Hargrave, and she showed us a flannel quilt she made to prove that even flannel does not have to be pre-washed. Her secret, she said, was machine quilting it appropriately before washing the quilt. Her quilt looked fine! However, having seen for myself how much flannel can shrink, that's the one fabric I will take the time to prewash before using.