Some context: The iPhone has a huge penetration rate in Switzerland (2.9 million devices sold for a population of 8 million people). Switzerland also has very good public transportation, held together by the train system of the SBB. And therefore, almost every iPhone user has the SBB Mobile App installed (http://itunes.apple.com/ch/app/sbb-mobile/id294855237?mt=8), 60-80% from what I heard. Which would put the install base to 1.5 to 2 million installations.
The elephant in the room is now this: Within this app, you are able to buy tickets. Train tickets, bus tickets, boat tickets. Not via in-app purchases, everything goes through the SBB ticketing system.
This has been working for three years now. Apple never blocked the app, despite it being in violation of some of the more prominent rules of the App Store.
My sources within SBB claim that there is no special agreement in place, mere toleration by Apple. I don't know if that's true, but one thing is for certain: The SBB has little interest of fighting with Apple on this front.
And Apple might not want to alienate such a huge user base, who would probably feel more loyalty to the SBB than to Apple, but that's pure speculation on my part.
On the other hand is the SBB fiercly proud of their design achievments, the clock in particular. Maybe that part of the SBB company (30 000 employees) doesn't care about electronic ticketing and will pursue Apple anyway.