I think the original thinking (when it was just ATL, ORD and DFW) was that there would be little connecting traffic from these cities, as they are all hubs for other airlines, so why would someone going to/from these cities choose to connect through EWR if they could just take a nonstop on DL/UA/AA. So these markets would primarily be origin/destination markets and thus not an inconvenience for any passengers being away from the "main" C terminal. Obviously CO has the historical data on what % of pax are O/D vs. connecting on these routes. I imagine that the other cities added also have high O/D traffic relative to connecting.

It also probably has something to do with CO trying to keep JetBlue's operations limited, but that doesn't answer the question of why these routes.

FWIW, CO is supposed to be instituting an airside shuttle bus between A and C.