i always take them outside & shake the heck out of them between cycles in the washer & a couple more times during drying- then you can take a lint roller to them too..personally i've never recommended raggy quilts for babies-
great for older kids
you can (trim)your frayed edges fairly close (like a chenille edge) that will cut down on the amount of (fluff) still fraying. some people use sweater shavers on them too-if your flannels are pilling. good luck --- i would recommend trimming the edges to about 1/4" and washing/shaking/drying/shaking again & again (if needed)