I've been looking into this problem; as here in UK we have prolonged rain and very salty roads for most of the year. The water runs down the vertical rubber seal between the small side window and the main side window, and continues to run down the door on the inside of the door rubber seal. You can often see where the water has tracked down near the dood latch when you open the door. Water is trapped on the inside of the door rubber and collects in the channel where rust forms cos' it has nowhere to drain. I proved this by filling a watering can with water and added a tiny bit of water based green dye and poured on my car. There was lots of green water trapped in the channel where rust appears.
I'm coming up with a little mod to allow the water to drain off properly. This is an example of one of the few bits of crap design in the car, but we can get round it!
Cheers Steve - UK