I'll start off by saying that I'm a fan of the paper if for no other reason than the sound and feel. My orthopedic doctor doesn't use paper on his table. It's the tall, non-adjustable kind with a vinyl top. I would imagine he rarely, if ever, has people sitting/ lying on it without underwear. I've never been on it without pants, even for a hip and knee evaluation. I have had my shirt off lying on it, but that's it. I don't even know for sure that they are cleaned between every patient. Kind of the same principle as a dentist's chair or the seats in the waiting room. Clothed people sit and lie on them all the time and you don't see people cleaning them.
I can't imagine not using paper at a family practice or ob/gyn or anyplace physicals might possibly be given. Think of receiving a rectal or gynecological exam and then immediately afterwards sitting on the end of a table that doesn't have paper on. Think of the big glob of lube that you would leave on the vinyl top. Then the nurse comes in after you leave, grabs a single Clorox wipe from the cabinet, and wipes down the entire table top surface. You know she's not going to spend any more effort than that cleaning. That big glob of lube that just came off your ass just got smeared all over that table top. Now imagine the next patient coming in, bare assed, and hopping on that table, and that happening multiple times a day. Ewww.
The paper is by no means perfect either though. As others have said, I'm sure certain things can leak through, or the paper tear. I've seen plenty of pictures and videos of legitimate exams where part of the patient is on the exam table not covered by the paper. I've had plenty exams myself where part of me, a leg, an arm, or something, is hanging off the side of the table touching the vinyl. I've noticed a few times that when I sit on the end of a table and rest my hands on the outside of my legs, they are usually off the paper. I'm sure bigger patients butt cheeks and back fat spill over the paper onto the vinyl all the time. There's just something about the sound of that paper though...