When you dry a rag quilt at home, it's a good idea to set the timer for 10 minutes and clean out the trap as many times as it takes to keep it from clogging. I'll do that even if it's the 2nd or 3rd time I've washed it.
When it's the first wash, I don't put it through an entire wash cycle. I put it through a rinse cycle only, by itself, then dry in 10 minute intervals. The second time I wash it, I put it through a regular wash cycle but with my towels. That way, if there is any lint released in the wash cycle, it will come off my towels easily in the dryer.
If you still have lint on your flannel, it's probably the flannel. I use the wide scotch type packing tape to get the fuzzies off.