I have an 04 with same problem. Rust thru under the filler cap. Also had an 05 that was showing bubbling paint when I sold it 3 years ago.
I thought I read somewhere that it was an inner fender issue that allowed moisture to get in behind to panel and they rust from inside out.

 

I had an 06 with overflow issues, and also rusting below the fuel door. I had 3 different body repair shops look at the rust, and they all told me the same thing: there is a double panel behind the outer rusting metal that traps the water/moisture, and therefore, there is no way to get behind the (outer) (rusting) panel for a proper repair/refinish. They said they could repair the outer rusted panel but it was almost a certainty that the rust would return. They all urged me to save my money as they could not guarantee a rust free area. I never explored a warranty or claim issue with Dodge. Ultimately, I traded in the 06 for a different 06 with low mileage.

 

Correction, my rust was at the junction between the bumper and the quarter panel, similar to the photographs in an earlier post.

 

My 08 rusted there and had the recall. They said they don't cover collateral damage from any recall. So if you have a bad wiring harness under the hood that starts a fire they wont paint the hood.

 

My 06 had the overflow and rust. Mine was built in November 2005 and I kept calling the Dodge Customer Satisfaction number and complaining about the overflow, then the subsequent paint bubbling. They finally heard me after about 3 years worth of calls and had me take it to the local Dodge shop for assessment. The first time the techs said the gas didn't overflow, I complained that they didn't fill it up. The service manager then went with me to fill it up and watched it overflow. Dodge then agreed to pay for the tank fix and the paint issue. When they when to repair, my Durango didn't have the 25 gallon fuel tank (that I pointed out numerous times over 3 years) it was supposed to have, it had an 18 gallon tank that they couldn't identify. The tank was replaced, but they found that the quarter panel was completely rusted through and they replaced the entire panel and painted. The cost to me was $100.00 that we negotiated. They originally wanted me to pay $500, but I kept after them that if the correct gas tank had been installed none of the repairs would have been necessary. My winning argument was that there was no other rust or paint bubbling anywhere except under the fuel door.

Long story short is keep complaining to Chrysler over and over and ask them to have the dealer at least look at it. They will eventually help. I started complaining in 2007 and they repaired/replaced in 2010.