Is there a problem with riding buses as opposed to trains, even if the bus functions as a
de facto train line?
They're special, dedicated buses that run as a train line. Underneath the official WTC/Seaport area hotels, the Silver Line is an underground tunnel that's even newer, nicer, and more secure (lots of video cameras) than a typical Boston subway station; the only difference is that buses run in it, not trains. At the World Trade Center station (
http://en.wikipedia.org/wiki/World_T...(MBTA_station)), for example, you enter the station through turnstiles like you would for a train, pay the train fare (a few cents more expensive than the normal bus fare), descend into the station underneath, board the bus, and then it takes you to South Station (1-2 stops down, or a 5 minute walk away), where you connect directly onto Red Line trains (one direct flight of stairs).
The Silver Line then emerges above ground to drive from downtown, through the third harbor tunnel, and directly to the door of each airline terminal at Logan. Currently, the Silver Line is free if you jump on it at the airport heading into downtown. Once it gets downtown (a 10 minute trip), it dives back into the dedicated tunnel that runs underneath the official hotels (as mentioned above). Although the free offer may not last until 2014, there is plenty of room for baggage on the Silver Line cars, and at about $2 it beats a $15-20 taxi from the airport.
I've done this many times and it is perfectly safe with many solo travelers (female included) using it as an easy way to get to the Seaport/WTC area, and to get to/from the airport faster than the Blue Line.