The rubber strip in the to of the Whispbars/Yakima bars isn't actually intended for you to remove, you just push it down in order to attach gear to it. Sometimes it's a bit stiff when you are sliding things into the track with the rubber in place, a bit of washing up liquid helps here.
It is possible to buy this rubber strip separately if you have removed it and would like a replacement. Click here for details and to order online.