The emergence of motorcycle-based ride-hailing services provides more transportation options to users in developing countries like Indonesia. However, many people currently believe that the availability of these new options threatens the demand for public transportation. This study aims to understand the latent factors that influence passengers to prefer bus service over motorcycle-based ride-hailing. The study includes 19 variables and applies a hybrid choice model by employing 703 bus passenger responses in Yogyakarta, Indonesia. Our analysis shows three latent variables that most significantly impact the selection of bus service over motorcycle-based ride-hailing: forced bus use, bus service quality, and favorable conditions for bus use. These three variables were influential enough to outweigh the potential time and cost savings of motorcycle ride-hailing. The results also indicate that the decision of which option to use is significantly influenced by users’ age and income. Lastly, results of our analysis show that future bus service demand will depend on how much buses can improve to meet users’ needs, if they are to win the competition over transportation options that can be booked online such as motorcycle ride-hailing.