I now warn people off booking.com after a really bad experience with them three months ago. I had used them for a large number of bookings for several years, but they treated me very badly and there seems no way of escalating things to a higher level. So I walked. Still use them to find hotels, but then use another engine to actually book, or book direct with the hotel.
hotels.com seems to be just as good if you need a booking engine.
I am told that booking.com charges hotels and apartments a commission of 19%, so it is often better for the hotel or apartment if you book direct and then you can negotiate a lower price while the hotel still makes more money than they would have done.