It's wise to prewash to avoid shrinking later. I sometimes even wash twice, to be sure I won't be disappointed by extreme shrinking.
If you plan to free motion quilt it, flannel can be harder to manipulate. I like using the supreme slider (slick sheet on the bed of the machine) to make it easier to move.
Flannel quilts can also be very heavy, so keep that in mind when choosing your batting.
RST