The surname Rafert is an Americanization of the German surname Röwer.  Other variation of this surname include Röver, Roewer, Röber , Rohwer, Raver, and Raefort.  Research suggests that almost* everyone with the surname Rafert is descended from one of two men who migrated from Germany to Indianapolis in the 1840s and 50s.

* I understand there are some African Americans with the surname Rafert, however I'm not sure how, or if, they are related.

Röver, Röwer(low-german) = Räuber, which in English translates to Robber
(From Hans Bahlow's German Surname Directory)