Unlike FxCop, the StyleCop tool out of the box only comes with Visual Studio and MSBuild integration; there is no stand-alone command-line tool. Still, as it's now open-source, we can look at the workings of the MSBuild task and see how to drive it directly.
Here is a proof-of-concept PowerShell script which can be used as the basis for a proper command-line tool or script; and as a preliminary "how to" to write unit tests for your rules. Well, they aren't going to be proper unit tests, since they'd have to touch the file system, but they can crawl over test source files in a dummy project in the StyleCop rule solution.
And that's all there is to it, really.