Using GTFS and Protobufs requires fairly advanced programming skills, and is not well documented, let alone for beginners. I wouldn't do this as a first project. You might have a look at
http://nycpulse.herokuapp.com/api, which isn't from the MTA but uses their data. It will give you easy to parse JSON like
http://mtaapi.herokuapp.com/api?id=120S. There are lots of tutorials out there to help you get started -- search for how to use a REST API.