Lee is right. To be included (and bookable) on 3rd Party websites (Hotels.com, Booking.com, Expedia, etc) the hotel pays a portion of the rate to the 3rd party website, 15% is actually quite low, some fees can be as much as 30-40%. Most of the 3rd party websites also require you to have rate parity with their site (ie. Hotel A needs to charge the same amount for the same room on their website). This means that when you book a room through a 3rd party website as opposed to the hotel's website you will likely pay the same rate but the hotel has to pay a significant portion of that rate to the 3rd party. If the rate differs between the hotel website and the 3rd party website it is usually an oversight by the hotel, not someone taking advantage of you or offering you a better deal.
When you contact the hotel directly (preferably by phone), you are very likely to get an even better price than what is listed on the hotel's website ... because of that rate parity deal (they can't advertise anything less than what you see on the 3rd party website) and because the hotel would love to not have to pay the percentage to the 3rd party website. For example, when I managed a local Best Western, we usually had a 'Manager's Special' listed in the rates that our staff could sell that was $10-$20 less than any advertised price. A guest would only get quoted this rate if you called the hotel directly and pressed the agent for your rate options, we couldn't list it on our websites or we would be violating the rate parity agreement with the 3rd party websites.
For the same reason, a hotel might not list ALL of their rooms on the 3rd party website. If they only list 20 double rooms but actually have 40 rooms to sell, for example, then they don't have to worry about the rate parity after that initial 20 room allotment is sold and they can sell the remaining rooms for as much or as little as they want on a given day.
As others have stated, these days you really HAVE to be on the 3rd party websites if you want to be visible at all. It's how most of us find our hotel rooms. Unfortunately, smaller family-run properties are really in a bind. They can't really afford those high fees to the 3rd party websites but they really can't afford to not be listed on their sites either. This is why a lot of smaller properties aren't listed on 3rd party sites. It is also why I always encourage people to search for their hotels on the 3rd party websites but actually make their bookings with the hotel directly, particularly if it is a smaller property.
For the sake of transparency, you should know that I've never dealt with booking.com as a hotel manager, so I can't speak to how their specific agreements with hotels work.