"Fährt der Bus öfter als der Zug?"
Translation:Does the bus run more often than the train?
Fahren seems like the best option for me. You could change the meaning slighty when you use 2 other common verbs in this context. First, Kommt der Bus öfter als der Zug? Does the bus arrive more often than the train? Its similar, because the bus does not only run but also arrive at the stops. The actions are somehow connected, but it clearly puts the focus on a different part of the entire scenario. Second, Fährt der Bus öfter ab als der Zug? Here we have abfahren / to depart and again a different focus.