Protégé 4.3 is now available as a release version and it comes with HermiT pre-installed. Alternatively, the file org.semanticweb.HermiT.jar from the latest HermiT release can be copied into Protégé's plugin folder. The next time you launch Protégé, HermiT will appear as an option in the Reasoner menu.
HermiT 1.x CANNOT be used with Protégé 4.0 since Protégé 4.0 is incompatible with the OWL API 3.0. HermiT 1.2.x works with Protégé 4.1 alpha and HermiT 1.3.x works wih Protégé 4.1 beta and more recent versions.
HermiT provides a command-line interface for common reasoning tasks, including classification and query answering.
HermiT can be used directly in Java and also supports the OWLReasoner interface from the OWL API. HermiT has native support for working with objects such as ontologies and class expression from the OWL API 3.0.0. More details and usage examples are available.