Rust is a very tricky issue to get warranty on. It all depends on where it is. Most of the time the dealer will tell you that the rust spot was caused by a stone chip or something to that extent. Of course if the rust is inside your trunk, then you could tell them to go suck an egg if they told you it was a stone chip or something.
I just went in for rust on my rear driver's window guide. It is definitely a bubble from underneath. I was of course told that it was a paint chip and that the labour to fix it would be approx. $90 Cdn. So I called the parts guy and asked how much a rear window guide was. $15 Cdn he tells me. I ordered it (just waiting for it to come in), and I'm just going to change it myself. I figured it wasn't worth the hassle to argue with them. Plus, last time I had my car in they gouged the crap out of my rear skirt and chipped the hood with what looks like something that was caused by dropping an air wrench.
Anyway, good luck with the rust. Like I said it's tough to argue no matter right you know you are.