The commission is paid by the yacht to the broker! It costs you no more to go through a broker. Boats who offer a lower price then they would provide a broker are soon shut out of the industry. Sometimes the yacht will give a discount on a week they want to sell or for repeat guests. Same with a broker.
They may offer a bit of their commission back to repeat clients or add in extras that the yacht does not cover. The commission rate is fairly standard throughout the industry. The yacht pays 15% to the broker on average, sometimes a bit more or less, depending on the week. It could be a bit more if you have a Travel Agent you work with as well as the Yacht Charter Broker.