Here we have a map of the commuter rail system from Wikipedia. It shows the lines in purple and the area the MBTA services in pink. The core city is a darker shade and the closer suburbs are in a middle shade. It's not essential to the traveler, but it gives the viewer a better idea of the area the trains service. Add a few major cities and it might give people a good impression of the system's size and all the people it can potentially service.
This is the Copenhagen metro area transit map. The subway lines are the thick yellow and green lines. The regional trains are the gray lines, and the local trains are dark blue. The most colorful lines on the map represent the S-Tog lines, the suburban train system most comparable to the Boston's Commuter Rail. In my opinion, the spectrum of color gives you a better sense of the number of lines and their distance.
You could argue that the MBTA Commuter Rail lines shouldn't be colored because they're part of a secondary system of lesser quality than the "T" subway lines. It's true that the S-Tog trains run every 20 minutes all day, except for peak-hours when they run every 10. It's also true that the S-Tog is all-electric (no nasty diesel fumes). Still, my hypothesis is that change can work differently. Instead of using colors to show the investments we've made, use colors to increase support for investment.
For a fair comparison, I've provided the closest official example I could find, the MBTA zone diagram.
Couple coloring the lines with thickening them (make them look important, like the primary means of getting around) and you've got a better map, in my opinion. Include some more lines to show the trains that don't run the full lines (e.g. North Station to South Acton rather than Fitchburg) and it's even better.
The colors will have a different psychological effect on each person, but I believe that one thing most everyone could take from it is a greater appreciation for the wonderful resource we have in Eastern Massachusetts known as the MBTA Commuter Rail.