Thanks JamesW for bringing this up. I unwrapped my FJR from hibernation, checked it out and sure enough, mine was missing the rubber flap as well. I ordered one from my local dealer, told him that this seems to be a problem with the 2013's and he gave it to me for free. Said he was going to bring it up with the Yamaha rep next time they talked.
For those who do not have the flap and waiting on back order, take a piece of heave vinyl cut to size and attach it. This is not a uniquely designed item.