the flannels i use are 100% cotton-
once in a while i may back a baby quilt with minkie-
i pretty much never make them out of fleece.
i make quilt tops out of quilting fabrics- flat cottons and flannels- i back them with flannels or minkie-or regular cottons depending on the baby- location- wishes of parents- what appeals to me at the time-
but flannel is cotton too- just a different weave & brushed to give it a softer face.