I would only use Booking.com (or others) as a last resort. After travelling for over 50 years, things surely have changed, but I feel that the larger booking sites tend to do more harm to smaller hotels/B&Bs/etc. It's true having a thought that if a business puts themselves on one of these sites, then that is their choice. However, some have no choice in order to get their name out there. After talking with owners of places I stayed, most have to pay 15-25% commission to be on the sites and receive no support from the site with no shows and late cancellations. When a business only has a small handful of rooms, it's very difficult for them to recover. I ask why they use them to the owners and most say what choice do they have. When you search for a place to stay, almost always Booking.com/Expedia/others are the very first results. There is no competing with that. I also know that larger hotel chains (Hilton for example) have had recent advertising campaigns to get people to reserve direct and not through Booking.com.
When I travel, I tend to look at the TripAdvisor reviews of a place and then contact the Hotel/B&B directly. In one most recent instance, the Booking.com rate I saw online for a place I wanted to stay in Italy was €420/night and when I went directly to the website, the direct rate was €300/night for the same room. I asked the owner about it and they said that Booking.com takes an enormous commission and they can't absorb it, so they pass it on to the customer. Obviously I booked direct.
I still do advise caution about business wanting money transfers, etc. If the places I stay don't take credit cards directly, then I tend to look elsewhere. I can always dispute the charges with my credit card company if there is an issue, however, in all my years of travelling, I think I maybe had to do this once. -Norman