The Alfresco repository provides the engine, the foundation, for document management. When you log in to /alfresco, and look around the folder structure, you are actually using a user interface that is connected directly to the repository.
Alfresco Share is a user interface on a different tier. While it still access the Alfresco repository, it does so at arm's length, using web scripts to process requests from the user and to display the results. Authentication is still handled by the repository, and Share trusts the repository to do the right thing.