Yes, the affiliate program covers your shopping cart as well as your member sign-ups.
To allow an affiliate commission on a product:
How to Assign an Affiliate Commission to any Shopping Cart Product
Products can be edited under Commerce Shopping Cart Add/Edit Products
Select the Product
Choose the product from the drop down menu or select 'New - Add New Item'
Under the 'Item Pricing' section select the flat rate or percentage and add the amount of the commission for both the 'Standard' and 'Super Affiliate' commissions.