Aerial robotics is a fast-growing field of robotics and in particular multi-rotor aircraft are rapidly increasing in popularity also out of the scientific community. However, designing autopilots for these vehicles is a challenging task, which involves multiple interconnected aspects. Hence, having tools able to show what happens when some new applications are going to be developed in unknown or critical situations is more and more important for the whole design process. The aim of this thesis is to show the role and the effectiveness of robotics simulators in flight control system design for multi-rotor aircraft (especially, quad-rotors) proposing a Software-in-the-loop (SIL) methodology. In particular, it will be explained, by using rather complex examples, how a SIL approach allows to detect and to manage instabilities that otherwise might not arise when considering the only MATLAB/Simulink simulations. On the other hand, such instabilities may not be just related to the complexity, accuracy, or detailed modeling of the simulated plant, but rather they may appear due to peculiar features of the final realization and, in particular, the software that will implement the control strategy. Indeed, aspects like synchronization, overflow, task communication, are all managed by libraries or tools available during the control design phase, and yet they are specific of the final code implementation. From such a perspective, SIL simulation has to be considered a valuable tool for discovering, in an earlier phase of the usual V-model process, those issues that Model-in-the-loop (MIL) simulation does not necessarily detect. At the same time, a SIL simulation, obtained by using realistic and detailed simulators give the opportunity of validating in an easy way the effects of modifying the control strategy for complex missions. That represents quite often the easiest way to tune the flight control system and to check its validity. Although advantages of such methodology are reasonable for the scientific community from a very general viewpoint, illustrative case studies can be of interest in particular if declined to the specific application.