The magnetic properties of Zn$_{1-x}$Co$_x$O ($x=0.07$ and 0.10) thin films, which were homo-epitaxially grown on a ZnO(0001) substrates with varying relatively high oxygen pressure, have been investigated using x-ray magnetic circular dichroism (XMCD) at Co $2p$ core-level absorption edge. The line shapes of the absorption spectra are the same in all the films and indicate that the Co$^{2+}$ ions substitute for the Zn sites. The magnetic-field and temperature dependences of the XMCD intensity are consistent with the magnetization measurements, indicating that except for Co there are no additional sources for the magnetic moment, and demonstrate the coexistence of paramagnetic and ferromagnetic components in the homo-epitaxial Zn$_{1-x}$Co$_{x}$O thin films, in contrast to the ferromagnetism in the hetero-epitaxial Zn$_{1-x}$Co$_{x}$O films studied previously. The analysis of the XMCD intensities using the Curie-Weiss law reveals the presence of antiferromagnetic interaction between the paramagnetic Co ions. Missing XMCD intensities and magnetization signals indicate that most of Co ions are non-magnetic probably because they are strongly coupled antiferromagnetically with each other. Annealing in a high vacuum reduces both the paramagnetic and ferromagnetic signals. We attribute the reductions to thermal diffusion and aggregation of Co ions with antiferromagnetic nanoclusters in Zn$_{1-x}$Co$_{x}$O.