My normal commute is completely by bike. However, when I visit my girlfriend in Providence (I'm in Boston) I will take the commuter rail in and ride the rest of the way.

Folders are allowed any time on the Subway or the Commuter Rail train and I've never really been hassled about it. (I've been questioned a few times while rolling my bike down the platform unfolded, but had no problems once I mentioned that it was a folding bike. In fact I didn't even have to demonstrate the fact). Now folders being allowed vs how convenient it is in actuality is a totally different matter. The commuter rail and subway get very crowded during rush hour. I can get by with my tikit without too much trouble, but if you brought a full size folding bike you would not have a very pleasant trip.