The easiest way would be to pass an FxCop project using the /project switch. For instructions on doing this, see the following post:
If the rule selections are the same across all projects, you can pass a template project file that contains your rule selections and simply pass the assembly to analyze via the /file switch.
You could also make use of the /ruleid switch, this enables you disable individual rules. For more information type fxcopcmd.exe / at the command-line.