There are several ways for a Buyer's Agent to be paid.  The most common way is exactly the same way other real estate agents are paid: The typical commission paid at closing is usually divided between the listing agent and the Buyer's Agent. 

The only difference is that the Buyer Agent agreement says that the Buyer Agent portion of the commission can be paid by the seller "on behalf of the buyer" and comes from the proceeds of the transaction. This statement secures your representation and discloses your representation to the seller.