Cyber-physical systems, used in domains such as avionics or medical devices, perform critical functions where a fault might have catastrophic consequences (mission failure, severe injuries, etc.). Their development is guided by rigorous practice standards that prescribe safety analysis methods in order to verify that failure have been correctly evaluated and/or mitigated. This laborintensive practice typically focuses system safety analysis on system engineering activities. As reliance on software for system operation grows, embedded software systems have become a major source of hazard contributors. Studies show that late discovery of errors in embedded software system have resulted in costly rework, making up as much as 50% of the total software system cost. Automation of the safety analysis process is key to extending safety analysis to the software system and to accommodate system evolution. In this paper we discuss three elements that are key to safety analysis automation in the context of fault tree analysis (FTA). First, generation of fault trees from annotated architecture models consistently reflects architecture changes in safety analysis results. Second, use of a taxonomy of failure effects ensures coverage of potential hazard contributors is achieved. Third, common cause failures are identified based on architecture information and reflected appropriately in probabilistic fault tree analysis. The approach utilizes the SAE Architecture Analysis & Design Language (AADL) standard and the recently published revised Error Model Annex V2 (EMV2) standard to represent annotated architecture models of systems and embedded software systems. The approach takes into account error sources specified with an EMV2 error propagation type taxonomy and occurrence probabilities as well as direct and indirect propagation paths between system components identified in the architecture model to generate a fault graph and apply transformations into a fault tree representation to support common mode analysis, cut set determination and probabilistic analysis.