I've seen this happen on a lot of different notebooks, not just MBs and MBPs. That is why as soon as I started carrying my current MB I placed a cloth in there. Even my old PB 12" had this problem.
With that said I am curious to see what Apple's response is if the OP decides to have Apple look at it.
I had a thinkpad that developed scratches due to jostling while in the trunk of my car. It got pretty scratched up around the pointing stick area. Since then I have always used one of these on all my laptops including the MBA :
http://www.shaggymac.com/index.php?main_page=index&cPath=3_4
To prevent this I use an iKlear micro-chamois polishing cloth that fits the 13" MacBook keyboard I have perfectly. I place this cloth on top of my keyboard before traveling. You could get any micro-chamois polishing cloth and just cut it to size.
Works great to prevent further marks, but it probably will not remove the marks that are already there; although you could try some iKlear Apple polish to see if it helps at all.
I've seen this happen on a lot of different notebooks, not just MBs and MBPs. That is why as soon as I started carrying my current MB I placed a cloth in there. Even my old PB 12" had this problem.
With that said I am curious to see what Apple's response is if the OP decides to have Apple look at it.
Are there cheaper alternatives? It seems pretty expensive for a piece of rag.