That has a lot to do with it. EWR is the most expensive (average cost per ticket) if you lump LGA/JFK together (which the BTS does since it compares cities and considers LGA/JFK as NYC while EWR is Newark). LGA has pretty high fares on a per mile basis, but the perimeter rule keeps the average flight distance shorter than EWR (and longer flights tend to have lower per/mile fares) while B6 keeps JFK domestic fares down.

Of course, on a specific route competition has a large part to play. Someone mentioned that US has the only non-stop to/from CLT, but CO also flies the route with COX. So no low cost competition.

Jim