Doctors are used to all kinds of questions and behaviors from patients. Take a few minutes and read some of the things that Emergency Room physicians have encountered. Also, keep in mind the things that they are exposed to in medical school and residency. Physicians are trained in germ theory and epidemiology as well (the study of transmission of disease)
Then, ask yourself: given all that, how would a physician be insulted if you ask a question that's designed to help ensure that a patient remain healthy and maintain patient safety? That's their job.
But, if you are worried about that, I'd suggest this course of action. "Doctor, I'm not sure about protocols and I am concerned about germ transmission. When was the last time that device was disinfected?"
Now, if a physician find that offensive, I'd suggest finding a different physician.