Depends on how they are rusting and exactly how the extended warranty is worded. Many do not cover cosmetic issues - you'll have to double check the warranty agreement to be sure. Unless there is a safety issue - they might not do a thing. Couldn't hurt to ask.
As for rusting steel wheels - I get them all the time. Especially when I lived in the "salt-belt" here in NE. Being down close to a marine environment - rusting is always an issue. Could also be an issue of how newer wheels are treated - used to be slathered with Cosmoline (a rust proventing gel, used to go on metal before an item was shipped via ship). Most new wheels just get a simple powder coating or couple of layers of paint. Also current brake pad friction material composition as greatly changed over the past several years - newer materials are more environmentally friendly and yield longer use, low dusting, and low noise - with minimal impact on performance. Problem is that this same dust is highly corrosive to wheel finishes. I used to run raw aluminum or magnesium wheels on the older pad materials (past 20 or so years) - never had a problem with brake dust, but with these newer materials, can even pit clear-coated alloys wheels.