I am not a urologist, so my input into this question is limited.
I discussed this question with several urologist colleagues, and some - not all - described this as a reasonable technique to examine the penis. Of course, some urologist may be rougher than others - leading to a negative encounter in your case.
If you are not comfortable with that particular specialist, obtaining another opinion is recommended. Imaging the penis with an ultrasound can be considered as well.
Followup with your personal physician is essential.
This answer is not intended as and does not substitute for medical advice - the information presented is for patient education only. Please see your personal physician for further evaluation of your individual case.
Kevin, M.D.
kevinmd_