Well, it really depends on what you mean with "comparing". Just comparing the different capabilities from one map to another? It also depends on how the Business Capability Maps has been created, if the Variant functionality has been used, there is an out of the box report that can show the differences in terms of which capabilities are unchanged, removed or added.
Directly on the Business Capability Map you can find some reports which can show you the structure and the different artifacts that realizes the different capabilities.
Another simple, but maybe not exhaustive enough, way would be to select several Business Capability Maps and use the Instant Report functionality to create a Matrix report that can show you which capability (components) are used on the first level in each map. This could be extended with a dedicated report that could show you all the capabilities used per capability map.
Compare can also mean that you would like to see how a given capability map has evolved over time - this is possible with the "Compare" function that you have in the "Activity Feed" of the Business Capability Map.
Also, there is some different reports that can show the structure and the fulfillent of each capability in a capability map. Also some reports exists to show the impact of projects on a given capability map.