Modern Air Traffic Management (ATM) concepts of operation require a strong interaction between agents such as human operators (pilots, air traffic controllers) and information technology systems (either on-ground or on-board). Although risks shall jointly be managed by all these agents, current risk assessment techniques are usually dedicated to only one class of agents (either human operators or IT systems). This paper addresses this issue. It proposes to extend Model Based Safety Assessment (MBSA) techniques originally developed to assess complex systems. This MBSA extension enables to assess how risk can be jointly managed by procedures and systems. The paper shows the methodology used and it presents lessons learnt from an aircraft trajectory management case study.