Zach Smith, one of the founders/makers is in both projects. Also, we (I'm RepRap developer) collaborate on designs to print and reuse each others technologies and ideas. Because both designs are completely open source, the can reuse whatever is practical and also differentiate themselves to be used in different 'market segments'. RepRap is meant to be more adjustable and modular, and meant to be able to replicate most of its own parts. The Makerbot doesn't have this requirement and can mostly be made on a laser cutter. Although several parts of the Makerbots are printed on Makerbots and/or RepRaps.
Erik de Bruijn http://blog.erikdebruijn.nl/categories/7-RepRap