Yes, the affiliate program covers your shopping cart as well as your member sign-ups.
To allow an affiliate commission on a product:
1. Under 'Commerce' choose 'Shopping Cart'
2. Select 'Add/Edit Products' from the shopping cart menu
3. Select or add product from the drop down menu and click the 'add/edit shopping cart item' button
4. Enter the commission amount in the 'Affiliate Commission Percent' and/or 'Super Affiliate Commission Percent (optional)' fields
5. Click the 'Apply Changes' or 'Add this Item' buttons
6. Provide your affiliate the url to create a link to send to their list