Rust where? Certain components are not painted from the factory. If its a painted part, push back on the dealer to see if they will do anything. In Calif don't really see that type issue, so no dealer experience on rust. What does the warranty cover? In the end if they don't help, I'd crawl under it, scrape, wire brush, prep and paint everything now while its new and rust hasn't really taken hold much, or gone crazy. It will be far worse to go back and do later.
2004 Wrangler Rubicon 4.0 w/Auto, 3.5" Rubicon Express Super Flex lift w/Currie Control Arms, RE Mono Tube Shocks, RE CV Drive Shaft, Engine/belly pan skid plate, Co2 Powertank. Hi Lift Jack.