The resilience of the transport system has been extensively researched in the past decades. Research has so far focused mainly on natural hazards as the main threat to the system. Current and future developments in the transport sector and beyond like automatization, digitalization, transition towards renewable energies and climate change will likely increase the complexity of the transport system and pose new challenges to ensuring the resilience of the system. Amidst these developments, the role of individual behaviour during disruptions will be crucial and needs to be better understood. In spite of the wealth of previous research on resilience, so far, no standard methodology for the assessment of the resilience at system-level could be established. In order to provide a roadmap towards such a methodology we discuss the intended functionality, structure and components of the transport system and propose several approaches on how to operationalize resilience metrics in a model-based framework.