Safety concerns expressed by micro-mobility users seem to practically constrain the use and flexibility of these new modes. This paper introduces a new, parametric agent-based modeling approach for simulating micro-mobility, using MATSim as a platform. Perceived safety is introduced as a factor, which affects travel behavior of micro-mobility modes in a car-dominated, heterogeneous, and perceived unsafe road network. For the purposes of the paper, different scenarios are simulated, using the city of Athens, Greece as a test bed, to examine the model performance and applicability. A universal scoring function based on travel time, cost, and safety, is proposed. This paper also discusses the concept of unsafe discontinuities. Simulation results show that an unsafe road segment of 500 meters long is sufficient to induce evident behavioral variations and hinder the practical use of e-bikes and e-scooters in the base scenario. The establishment of a cycle-friendly road network leads to significant changes in the chosen routes and decreases the average trip distance for micro-mobility users. In this case, the simulation process is guided by perceived safety, primarily focusing on formulating safer paths for micro-mobility mode users. Nevertheless, the routing behavior of car users is not modified due to the spatial uniformity of safety perceptions in a car-dominated road environment.