Flannel works well in lots of quilts and is often 100% cotton. Just be aware that flannel usually shrinks a lot more than other cotton fabrics. Unless you are planning on a great deal of quilting, it's a good idea to pre-shrink flannel before using it in a quilt. I like to run it through the washer and dryer twice, and I don't pre-wash other cottons.
It is also a good idea to heavily starch flannel after pre-washing. Starch adds a lot of stability so that pieces don't distort with handling (and so the backing doesn't distort while you are quilting). Flannel is much stretchier than other cotton fabrics if it is not starched.
In general, cotton fabrics are easier to handle than polyesters. Polyester fabrics tend to be slippery, making accurate cutting and piecing more difficult. They also tend to ravel more than cotton.