The van der Waals ferromagnet Cr$_2$Ge$_2$Te$_6$ (CGT) has a two-dimensional crystal structure where each layer is stacked through van der Waals force. We have investigated the nature of the ferromagnetism and the weak perpendicular magnetic anisotropy (PMA) of CGT by means of X-ray absorption spectroscopy and X-ray magnetic circular dichroism (XMCD) studies of CGT single crystals. The XMCD spectra at the Cr $L_{2,3}$ edge for different magnetic field directions were analyzed on the basis of the cluster-model multiplet calculation. The Cr valence is confirmed to be 3+ and the orbital magnetic moment is found to be nearly quenched, as expected for the high-spin $t_{2g}$$^3$ configuration of the Cr$^{3+}$ ion. A large ($sim 0.2$ eV) trigonal crystal-field splitting of the $t_{2g}$ level caused by the distortion of the CrTe$_6$ octahedron has been revealed, while the single-ion anisotropy (SIA) of the Cr atom is found to have a sign {it opposite} to the observed PMA and too weak compared to the reported anisotropy energy. The present result suggests that anisotropic exchange coupling between the Cr atoms through the ligand Te $5p$ orbitals having strong spin-orbit coupling has to be invoked to explain the weak PMA of CGT, as in the case of the strong PMA of CrI$_3$.