iOS 9 and OS X 10.11 El Capitan debuted with transit maps for a variety of North American cities, but Boston was left off the list. It didn’t take Apple too long to fix that, though. The company has updated its maps data with transit information for Boston commuters. If you plan to use the MBTA or Commuter Rail to get in and out of Boston, you can now use Maps to plan your route.
There are, of course, third party apps that have filled the gap quite nicely, like Transit. Still, it’s convenient to use built-in apps, and Handoff integration makes it convenient for you to plot your route on your Mac then transfer it to your iPhone.
You shouldn’t need to do anything to see the new content — it’s all server-side on Apple’s end.