I disagree. Take your example of West Roxbury. Google puts biking time from West Roxbury downtown as 51 minutes. The commuter rail, which has about hourly weekday service and no weekend service, is scheduled for 35 minutes to South Station. So, if your starting point is literally at a commuter rail station and your end point is right next to South Station and there is a train pulling into the station right now, then yes, it is quicker.
A bus and the orange line is going to take you an hour, not counting waiting time. So, if there is not a commuter rail train pulling in right now and your end point and starting point are not next to the commuter rail stations, it is going to be quicker to bike. Not to mention if you are traveling between West Roxbury and Brookline, Allston, Brighton, Cambridge, Somerville, Dorchester, Mattapan, South Boston, North End, etc. it's always going to be quicker to bike.