John is correct, you must have a CassetteConfiguration class to tell Cassette which assets to create bundles from.
Cassette's Bundle.Reference helper only finds defined bundle and asset paths.
Existing .min.js and .min.css will be used by Cassette. The real issue is that if there are both min and non-min files present, both currently get included in bundles. I'll be addressing this issue in v1.1. For now either delete the duplicate files, or use a custom FileSearch object in bundles.Add(...) to exclude the files.