How do I collect shipping fees?
One of the driving principles behind Drupal Commerce is to keep the core as small as possible, providing the basic systems required for an e-commerce website. The core systems can be easily extended to add additional functionality as necessary. As such, while the core of Drupal Commerce does not contain shipping modules, it provides the systems required to support them: a generic line item system, a pluggable checkout form, and a user interface for determining the conditional availability of shipping services.
Even though we didn't bake the shipping modules into the core package, we give them special attention as "essential, non-core" contributed modules. The primary work right now is centered on the Commerce Shipping module, which defines a checkout pane for letting customers choose a shipping service and adding an appropriate shipping line item to the order upon checkout completion. Shipping methods are defined by additional modules that plug into this shipping system, and their availability during checkout for a particular order is determined via the Rules interface. This functions in much the same way as the core payment selection checkout pane.
Development of this module is ongoing, so we will update this page as Commerce Shipping matures and other modules are written to integrate it with services such as UPS and FedEx.