The appeal of affiliate marketing is that it involves minimal risk, with no cost to set up, you pay the affiliate only when they get you sales on your store. If the margins are sufficient then, affiliate marketing virtually costs no money. It is cheaper than traditional advertisements.
When you set the default commission rate to say 5 percent. When an affiliate's referral is used to buy shoes worth $100, the affiliate, in this case, will earn $5 as a commission on it.
When the product commission rate is set to 5% for the shirt and 8% for the shoes and a visitor buys both of them. Then the affiliate referral used to buy the $50 shirt, will earn the affiliate a $2.5 commission and for the $50 shoe, the affiliate will earn $4 in commission.