The values you consider acceptable for various coverage metrics are another important kind of filter.
NCover reports coverage statistics with color coding based on the thresholds provided in these settings, which are set with some reasonable default values when you create a project. You can reset these values at any time from the Project Home view by by clicking and then clicking Reset to defaults on the thresholds tab.
The NCover summarize command line functionality for the NCover server uses the thresholds set on this tab to fail the build.
NCover checks the thresholds against that execution, printing out any that fail.
If any thresholds fail, NCover will return an exit code of "1" to indicate an error.