Recent experiments for linear magnetoelectric (ME) response in honeycomb antiferromagnet Co4Nb2O9 revealed that the electric polarization can be manipulated by the in-plane rotating magnetic field in a systematic way. We propose the minimal model by extracting essential ingredients of Co4Nb2O9 to exhibit such ME response. It is the three-orbital model with xy-type atomic spin-orbit coupling (SOC) on the single-layer honeycomb structure, and it is shown to reproduce qualitatively the observed field-angle dependence of the electric polarization. The obtained results can be understood by the perturbative calculation with respect to the atomic SOC. These findings could be useful to explore further ME materials having similar manipulability of the electric polarization.