The revolution of Remotely Piloted Aircraft Systems (RPASs), both in the commercial and the research field, has accelerated the arrival of innovative and complex services to the civilian environment within non-segregated airspace. The extensive deployment of these services will still require solving relevant challenges in several topics, such as regulation, security, or diverse technical defiance. In particular, the services to be provided increasingly demand network resources and performance improvements. This scenario will be strongly exacerbated by the upcoming resources provided by the 5G/6G architectures, where Remotely Piloted Aircrafts (RPAs) will likely support multiple communication interfaces and will be able to establish multi-hop network connectivity with numerous devices leading to an unprecedented hyper-connected RPA environment. In addition, future RPASs will have to enhance the management of their connectivity capabilities to comply with the latest regulations, which demand an uninterrupted link for the Control and Non-Payload Communications (CNPC). This article presents a flexible Communication Infrastructure Manager (CIM) based on Software-Defined Networking (SDN) and virtualization technologies capable of handling the complexity inherent to this ecosystem and being adapted to different operation requirements to cope with all these communication challenges. Finally, the article shows several validation experiences to demonstrate the potential of the CIM versus the standard approach.