Bottom corners near the glass or the bottom of the frame? The corners near the glass is a common spot for rust. It's caused by dirt sediment getting behind the gasket piece that covers the slot. Sediment absorbs water and holds it there till the metal rusts. The way to prevent this is to wash the Jeep occasionally and make sure to spray into the gap area. Coating that area with an extra layer of paint wouldn't be a bad idea either.
If you mean the frame, then that's another problem all together. When the jeep is painted it isn't painted with everything off. This means some parts go unpainted or some places are very lightly painted like behind the windshield hinge on the body. Also, you need to make sure water isn't leaking into the windshield frame from either up top or on the sides. (see my 'it still leaks' thread.) Water trapped in the frame will cause rust since the inside isn't painted. Also, if your cowl seal is old it will retain water like a sponge and hold it there. Since the instrument panel isn't usually painted, it will rust under the cowl seal and cause the jeep to leak from the dash as well...
