sbm12,
Let's look at the other carriers on the BOS to DCA route as far as same day changes. Also I'm chiefly comparing the elite experience because whatever airline I fly with I'm going to be elite based on how much I fly:
US, predominant carrier:
Offers all elite levels the ability to "move up" to an earlier flight at no charge, though unofficial practice, is you can also use this to go on a later flight. Elites are confirmed on the flight or put on standby if the flight is full. Nonelite pax generally pay a fee for this service.
Analysis: If your not an elite, JetBlue's $40 is a better bargon. If your at least Silver Elite, free is better although you can't make these US changes as an elite fore free on the phone where as I believe the B6 $40 is available by phone.
Delta, also provides RJ service on route:
For Gold and Platinum Medallion members, can confirm a same day confirmed SDC with in 3 hours of the original flight at no charge. Silver and general members pay an SDC fee I think $75. SDC can be confirmed by phone or at the airport. Elites can have free standby if no SDC seats are available.
Analysis: Again B6 for $40 is better for a non elite or a Silver. But Gold or Platinums free is better. The drawback, you can only Delta SDC with in 3 hours not anytime for $40.
American, RJ's Eagle on the Route
General members pay a fee I think $50-$75 to confirm a change with in 12 hours of the new flight time. Elites can standby for free but officially they are still charged if they confirm a same day change. I don't think AA waives this fee officially even for Executive Platinum members.
Analysis: The B6 $40 fee is lower, though the elites can standby on any same day AA flight for free.
Overall Analysis:
There is no question if you are not an elite, particularly a Gold or Platinum elite, that the B6 $40 fee is lower.
But for frequent shuttle flyers, DL and US offer better free flexibility. I give a slight nod to DL because they allow the changes even by phone with in 3 hours of a same day earlier or later flight, although unooficial practice is for US to honor the same thing at the airport even for later flights free for all elite levels.
I don't like AA's policy of even charging Executive Platinums the same day confirmed fee, and thats why I likely wouldn't fly AA, plus they don't provide complimentary domestic upgrades like nearly every other legacy carrier. And there is nothing about AA first class domestically to make it so special that I'd be willing to pay more for it rather than get a free elite upgrade on CO, DL, UA, or US.
While Southwest is not on this route yet, I really value there no change free policy. If I was not sure if I wanted to fly back say DCA to BOS on Sunday morning, Monday morning, or Monday evening on Southwest, I could book a seat for all three flights. Then the 2 reservations I did not use, I could use the credit for future flights at no charge. Eg I could book all three seats at the $69 price, and thus never have to pay a $200 fare difference.
I realize your average person wouldn't like this, but I know the system and I wouldn't really have a problem booking the extra space to save money if I really wasn't sure on when I was going to travel, and especially if Southwest were strict with their fare difference provisions. But if I fly every week with Southwest, same gates same citys same agents, I'm sure they would put me on earlier flights and somehow the extra fare mysteriously of course would not be collected.
I have no doubt that Jetblue waives some of these $40 and $100 change fees at the airport in certain circumstances for both frequent and infrequent flyers. I'm sure also the standby rules are not consistently and strictly enforced at JetBlue.