If the commuter rail is not convenient they could park at the end of the T, e.g. Alewife, BC etc.

But now they need to pay for the car anyway, so you're left balancing the comparatively small cost of parking + extra gas + extra mileage against inconvenience of switching transit methods + cost of transit.

There's many other factors, too, which could influence things in either way: total time spent commuting, whether you hate crowded spaces and prefer to sit alone in your car, whether you can be productive (eg: phone call, working on laptop, doing email on phone etc) or want to be able to read.