DC is one of the best layouts for rail connection in the US. (Though it's even nicer that you can walk right down to Crystal City!) I also liked the location of St. Louis' light rail. They have a nice way of gouging infrequent riders - tickets are 3 times as expensive if you buy them at the airport. But you can use 10 ride and other tickets you buy elsewhere. The Orange Line at MDW is a great recent airport train Quick service to downtown, plenty of other connections, and all on the same transit fare system. (But you have to walk through the parking garage to get there!) That said, I take a bus from my house to MDW.

Boston is downright annoying. A bus to the train, and then almost surely a transfer to another train. And another one if you want to get to south station - and this to go just a few miles. At least you can do all that for a buck.
Charging $5 for the Airtrain at JFK seems excessive. Time will tell if things pan out. A train will always bring out more riders, but it would be nice to have something like CDG or Zurich where trains actually go somewhere directly from the Airport.

I used to do BART->SFO, Caltrain->SFO, and Amtrak->SFO and Samtrans->SFO. BART->SFO is now more direct... sometimes. However, on weekends, it still requires a transfer, not much better than the old BART->Samtrans transfer. Caltrain to SFO got a lot more expensive and inconvenient. The free shuttles timed to meet the train are replaced by BART running every 20 minutes. Amtrak SFO went from train->BUS to (on weekends) Amtrak->Bart->Bart->Bart. Luckily the Samtrans SFO bus is still there!