If you can find it, there is a product called 3M Pink Filln Glaze. This is what they use after buffing out a car to fill in the swirl marks and will make your rubber mouldings shine like new. Any body shop material shop should have it.
hehe, probably a better idea than replacing them...i was just sayin' cuz i had to replace one of mine when it got dented a while back and it cost a sh*tload just for a molding!
oh yeah, if you just gonna paint them got to be careful because they are VERY hard to remove without damaging the side moldings...those things are very fragile and aren't meant to be removed and placed back on!