In the SF Bay Area, Caltrain is aboveground and is more than quiet enough to call into meetings. Think NYC's MetroNorth, there's no reason you wouldn't be able to make a call until you get into the tunnels near Manhattan. On the other hand, BART is underground with signal repeaters just about all the way through - but it's very noisy so you could call in and listen but probably not contribute.

If your transit system is underground without repeaters though, I agree that you're out of luck. I can't imagine trying to take a call on the T.