Unless you have parking included, work somewhere outside of downtown Boston, or carpool, it's almost certainly cheaper to take the commuter rail compared to driving. Regardless, even if it isn't cost effective for you personally, it is for many people who commute into the city a couple days a week but not often enough to need a monthly pass. As for the commuter rail zones, the Newburyport/Rockport line isn't the only one with multiple stops within the same zone.