IMHO, since it's within warranty, the entire car was supplied by VW, and thus should all be covered by said warranty, that it should be 100% covered by warranty.
Even though they ARE just wheel covers, it shouldn't matter. It's a part that was on the vehicle when sold.
... having said that, if it were my car, I'd more likely go one of the following two routes:
1 - Plasti Dip the covers. Why not have a little fun and see what kind of cool combination looks I can come up with. If they end up all sucking, then I go with...
2 - Aftermarket Alloy/Aluminum wheels. TireRack has some pretty decent ones that fit that car for around $100 each. Maybe see if the dealer will credit you back a few bucks toward them for the defective wheel covers?