I strongly prefer all-cotton batting.
The problem with cotton flammability comes mostly with clothing. Loose cotton clothing will go up in flames very quickly because air can get to it from all sides (think cotton nightgown). Cotton clothing is not a flammability problem if it is close-fitting, as in long-johns. A quilt will not burn unduly quickly because the cotton batting is thick.
Polyester is not without its problems. The fumes given off by burning polyester are not good. Also, polyester melts and can cause deep burns if it melts onto skin.