If your microwave has started rusting and is flaking off inside I would get rid of it. There is no fixing that. You really don't rust falling in your food and then eating it, that could be pretty toxic. I say go get a new microwave.
once rust starts it lives inside, the baked on enamel has failed.best to dispose of with an electronic recycler- you will get a few dollars for the metal then get the most enery efficent model you can .good luck0 ironman@ bomdesign