Well-known for its efficient computing capabilities, FPGA-based architectures also have the potential for high flexibility with dynamic reconfiguration features. Yet, writing applications on these architectures is laborious, poorly portable and hardly scalable to multi-user and/or multi-FPGA systems, mainly because of a mixture of application related code and flexibility management code. In this paper, we propose a new abstraction layer, called Hardware Component Manager (HCM), which clearly separates the allocation of a hardware function from the control of a reconfiguration procedure, and guarantees the security of coexisting configurations. The implementation of this HCM layer on realistic simulation platforms demonstrates its ability to ease the management of FPGA flexibility while preserving performance and ensuring hardware function protection. HCM implementation and its simulation environment are open-source in the hope of reuse by the community.