Two-dimensional (2D) Heisenberg honeycomb ferromagnets are expected to have interesting topological magnon effects as their magnon dispersion can have Dirac points. The Dirac points are gapped with finite second nearest neighbor Dzyaloshinskii-Moriya interaction, providing nontrivial Berry curvature with finite magnon Hall effect. Yet, it is unknown how the topological properties are affected by magnon damping. We report the thermal Hall effect in Cr$_2$Ge$_2$Te$_6$, an insulating 2D honeycomb ferromagnet with a large Dirac magnon gap and significant magnon damping. Interestingly, the thermal Hall conductivity in Cr$_2$Ge$_2$Te$_6$ shows the coexisting phonon and magnon contributions. Using an empirical two-component model, we successfully estimate the magnon contribution separate from the phonon part, revealing that the magnon Hall conductivity was 20 times smaller than the theoretical calculation. Finally, we suggest that such considerable suppression in the magnon Hall conductivity is due to the magnon damping effect in Cr$_2$Ge$_2$Te$_6$.