A hybrid quantum system consisting of spatially separated two-level atoms is studied. Two atoms do not interact directly, but they are coupled via an intermediate system which is consisting of a superconducting flux qubit interacting with a mechanical and an electrical resonator which are coupled to one of the atoms. Moreover, the superconducting flux qubit is driven by a classical microwave field. Applying the adiabatic elimination an effective Hamiltonian for the atomic subsystem is obtained. Our results demonstrate that the entanglement degradation decay as well as the fidelity decay in the dispersive regime are faster. Moreover, the driven field amplitude possesses an important role in the entanglement and fidelity evolution.