If you want to use Hibernate with Maven, do the following:
Create a new Maven project and skip archetype selection. Add following dependencies: hibernate-core, hibernate-entitymanager and your JDBC driver.
Select project properties, Project Facets, choose JPA and edit JPA configuration: Select Hibernate, disable library configuration and select your database connection in Eclipse. This will create META-INF/persistence.xml file. Goto Connection tab, choose transaction type "Resource Local" and populate configuration from your Eclipse connection.
Now you have your project fully configured for work with JPA.