Regardless of whether the flights make money or not, BOS-EWR will help build loyalty to JetBlue for BOS-based O&D passengers (like BOS-DCA). I think it's a brilliant move.
BOS is a huge O&D market, of course, yet not a fortress hub for any airline. So there's a big hole for a "hometown" airline that will build loyalty in New England. Seems to me like JetBlue is trying to fill that void.