I have used booking.com several times, meanwhile it's true don't chekc or can't check every room they got on their site, I have both good and bad experiences, however I can say, anytime I had a problem, their customer service sorted it out very quick.
The only thing I wish they wouldn't let hosts to charge for deposit by cash. You give a large amount of money to someone, there is no record about the transaction, if the host keeps it is nothing you can do, it is only cash hand to hand. That stopped me several times to book some nice rooms. I don't mind to pay deposit but if you can't provide any record of the transaction then no thank you.