I don't know much about EJBs, but I do know that the ORM layer needs to be aware of the relationships between entities corresponding to the relationships in the database. Managing associations is one of its main advantages.
Relationships in your entities and ORM mappings can be one-directional or bi-directional. No one says that a User object needs to be aware of all its comment objects. The UserComment can have a one-directional reference to the User mirroring the underlying foreign key reference, but the User can be completely unaware of Comments or UserComments. That's one of the reasons why fetching one entity does not bring the whole database with it. Lazy loading is another.
If a comment is just a comment and cheese is just cheese, why do you want to put your comments in different tables? If you don't care where the comment came from, just as you don't care which pizza your cheese ended up on, then just put them in one table. But as soon as you start caring about which pizza got which slice of cheese, or who made what comment, and you start making that differentiation in the database, you need to reflect it in your ORM mappings, or modify the ORM code itself.