I have been using booking.com for more than 3 years and I have made dozens of reservations using their service. In most cases it has worked out well. I have stayed at some amazing places that I would probably not have found otherwise.
You do need to read the conditions of the booking carefully. And read the reviews, especially the recent ones. Be cautious using them if it is less than a week before your stay. I've had a couple of reservations canceled, by the hotel in this situation and it has been inconvenient. However booking.com did contact me and offered an alternative booking.
Part of the problem is that the "cancel for free" reservations allow travelers to overbook and then cancel in the last few days. This makes for a chaotic situation.
I would also caution travelers to use caution when booking at smaller establishments, and especially apartments. Finding the person who will give you the key can be time consuming, especially if you arrive after a long trip with a delayed flight after normal business hours.
On the plus site the range of choices available, the search features, the maps, and the reviews make booking.com a powerful tool for finding interesting places to stay. booking.com also keeps a history of where you stayed and when in your account which is nice if you are returning to a location.