i make lots of cotton with flanne quilts- they are wonderful quilts- i make lots of quilts- i use many different fibers===wool, cotton, silk, velvet, corduroy, denim...and yes- i even put them all together sometimes- the key is to pre-wash and make sure your fabrics will play nice together. my wool applique quilt is felted wool appliques on a fabulous double sided Benartex flannel-
it washes up wonderfully...flannels tend to (generally) shrink the most- because they have a looser weave than the cottons you are used to using- but beyond that- they generally go together very well