Tutorial
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
Add/Edit Products
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'
Affiliate Commissions
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.