Finite element simulations of rubber protective coatings with different structures under two dynamic loading cases were performed. They were monolithic coating and honeycomb structures with three different cell topologies (hexachiral honeycomb, reentrant honeycomb, and circular honeycomb). The two loading cases were a dynamic compression load and water blast shock wave. The dynamic mechanical responses of those coatings under these two loading cases were compared. Finite element simulations have been undertaken using the ABAQUS/Explicit software package to provide insights into the coating's working mechanism and the relation between compression behavior and water blast shock resistance. The rubber materials were modeled as hyperelastic materials. The reaction force was selected as the major comparative criterion. It is concluded that when under dynamic compressive load, the cell topology played an important role at high speed, and when under underwater explosion, the honeycomb coatings can improve the shock resistance significantly at the initial stage. For honeycomb coatings with a given relative density, although structural absorbed energy has a significant contribution in the shock resistance, soft coating can significantly reduce the total incident impulse at the initial fluid-structure interaction stage. Further, a smaller fraction of incident impulse is imparted to the honeycomb coating with lower compressive strength.