Anyone out there the owner of such a company?
I noticed you are all available through several brokered sites and some have their own website in addition.
Just trying to figure out your costs within your prices.

How are they taking their cuts? Is there anyone who doesn't book through a broker?

Crewed charter boats are either owned by a company, or individual. They are not "owned" by clearinghouses, brokers. Any person in the world who has a boat can put it up for charter. To Market to the broker in the broker network, they get a clearinghouse. There are several of these, a clearinghouse "mostly" holds a boats calendar, as well as holds the charter money in escrow. Brokers will call clearinghouses looking for availibility on a particular charter boat and can hold it if they have a hot prospect. Once they confirm it they give the money to a clearinghouse who holds it until the time comes to pay it out to the boat for a charter.
Typically if you are selling through the broker network, you have a couple opportunities a year to attend a boat show to show off your boat and yourself and the good brokers, keep up to date on what you and your boat are like. Like everywhere else, there are good and bad boats and brokers. One of the problems with the internet is there may be information on many broker or boat websites that is not up to date.
Some boats sell both through the broker network, and their own marketing. Makes sense to get all the bookings you can! Some only sell through brokers, some do not sell through brokers at all!
So, a broker is like a travel agent, and they take a commission from the boat on each charter they sell. Typically 15 to 20%. The clearinghouse takes another small percentage for their services. Probably largest long established boats, or very small boat tend to sell directly more often. Can you get it cheaper, technically, no. A boat will not sell it cheaper than to a broker so they will not be blackballed. However, MOST brokers and owners offer different incentives, IE no credit card processing fees, repeat discount, free taxi, free scuba etc etc, and the boats will also sometimes offer and additional freebie or discount to book as well.
There are a lot of people who do not book through a broker. With the internet it becomes more and more every year.
Do your homework, and talk to brokers and boats where possible to get an idea what really suits you