CER's purpose is to keep reference fields synchronized with each other. For example, if you have a node ("Alice") with a user reference field, and a user ("Bob") with a node reference field, and you make Alice reference Bob, CER will automatically give Bob a back-reference to Alice. If Alice subsequently dereferences Bob, Bob will automatically deference Alice. Or, if Alice is deleted, Bob will lose his reference to Alice. CER does all this transparently.
CER is a powerful module. It lets you create relationships between different "reference-type" fields. A reference-type field is, simply, any kind of field that references another entity. Out of the box, CER supports Entity Reference, Node Reference, User Reference, and core Taxonomy Term Reference fields. It also includes a pair of add-on modules supporting Profile2 and Commerce Product Reference fields. CER also has an object-oriented plugin API that you can leverage if you need to support other types of reference fields or alter CER's behavior. (More information about CER's API can be found in cer.api.php.)