That is not a rubber moulding part. It's a front roof rail cover that covers the mounting bolts for the roof rails.
I know - I installed a set of roof rails myself.
Strange how it comes off easily on yours - mine took some prying...
Here are your options:
1. Take it to your dealer and see if it is warranty issue.
2. Buy a set of roof rails and install it yourself.
3. Find a set of rail covers for sale on eBay or Craigslist - someone may be selling them....