Surely they must be using the Google Maps API as part of their service, and Citymapper is an alternative to using Google Maps.
The TOS for Citymapper states that
We use third parties, such as Transport for London, Metropolitan Transport Authority and other transport agencies, Apple, Google, OpenStreetMap, Foursquare, Yelp to provide data on which the transport information and recommendations in the app are based. We and our partners try to make sure that the data is correct and up-to-date...
So they must have agreements with those companies and government entities to access the data.