At some point, either the windshield was replaced with the wrong sealing product, or you just live in an area known for rust. The sealer will not stick to the rust, and you only option is to pull the windshield, and sand it down, and hope there is enough metal to bond correctly.... OR, to weld in a new piece of windshield channel.
As far as the seals go, your going to have to call around to all the windshield companies in your area, and see if you can locate someone local that has the windshield, and seals, in stock, or can get them.
Thats really the only options.
You must fix the rust, as the windshield sits in a location, that inbetween the baking sun, rain/snow and other environmental effects, it will only get worse, and at a very speedy rate.
Although only the first 7 minutes are directly related to your question, later in the video, he goes into detail about the other things that you may not have even thought about for damage (carpets, EVAP, etc).