The secondary reporting of the research in dentistry.co.uk is actually pretty reasonable and unsensational. A couple of points, though. I run a medical research database for my day job, and so have lots of contact with academic, peer reviewed journals (over 700 papers published on our data) and it's clear to me that 'learned' journals are no less susceptible to the attractions of a juicy, newsworthy story than any other sector. This is a story that, whatever the facts, makes good copy.
Also, of course, dentists have to take much more care over transmission to and from patients than the public at large, due to the volume of patients, the frankly disgusting state of some and the ever present threat of litigation. I have had the misfortune to have to visit the dentist a lot more than most, and I am pleased and reassured that all the dentists I have seen take hygiene very seriously.
However, the real nub of the problem is that the human mouth is, if you analyse it, a pretty disgusting place (ask an A & E nurse what they do if a victim of a human bite comes in). The fact is, though, in most cases our bodies cope with exposure to all sorts of nasties, and I think it is the same with things we come into contact with via musical instruments. There is always a risk, but there's a risk to everything in life.
A final thought, on risks and benefits. Kissing. When you're about to give someone a snog (assuming you haven't been repulsed by breath that would cut steel) do you clean and disinfect them first?