Higher compared to what? There are plenty of smaller hostels/hotels which don't even bother to have their own website (only some FB page, and Booking.com listing)
Booking.com has a higher chance for errors compared to hotels' direct bookings since its information is secondhand and unreliable. For the hotels with direct booking avenues, why use booking.com?
Because booking.com answers the question "where can I stay given place, date, and budget"? While direct access can only help you when you already know where are you going. The latter is fine if you travel to the same place many times, the former is more universal. As for reliability, I dunno, I used to travel a lot, and in my experience troubles mostly come with a particular destination, not with the method of booking. I.e. if a hotel is unreliable (poor business culture, or overbooking, or whatever), it's unrealiable.