Pull the interior panel to see if it's rusting from the inside or just salt accumulating in the plastic panels causing the rust.

From the inside it is most likely a combination of the window weatherstripping and the drain holes in the door clogged. That's a bad thing because it makes the rust repair much more difficult.

I have also seen the panels being loose cause them to vibrate and rub into the paint. This causes the surface rust along the top of the plastic and eventually allows moisture to build up the entire length of the panels. This is not so bad since it is usually just surface rust. Much easier to sand, treat and re-spray.