I'm having a hard time with some of the animosity towards medical personnel here. I hope that anyone who felt I was out to harm their child would take their business elsewhere.
I cannot agree more about giving preteens and young teens the opportunity to speak with me privately. In my state kids 12 and up can consent on their own for care for pregnancy, STD testing or counseling, birth control, mental health issues or substance abuse. When I do a sports physical for a 7th grader, I merely mention that as they get older they may have issues they wish to discuss, and that they are welcome to ask here without fear that I'll be reporting immediately to their parents. I always tell teens that I hope they'll discuss any issues with their parents, and that it's always best if their parents know what's going on in their lives, but that they can get care from me for birth control, or STD testing, or whatever on their own. An awful lot of kids tell me in private that they are sexually active and wondering about preventing pregnancy, or they just started smoking, or whatever who wouldn't say the same in front of their parents. And unfortunately, not every young teen has supportive, understanding parents and might be in physical danger if their parents knew they were having sex, or drinking, or whatever. Having a neutral place they can discuss things is helpful for a lot of teens. Knowing ahead of time where they can go if they have a sudden need for birth control, or are feeling depressed or whatever
I also take a few moments alone with the parent to make sure they don't have any particular concerns, and to clarify for them that I'll be telling their child about their right to confidential care.
I also agree that any patient has the right to know why I'm suggesting any part of the exam or tests or whatever. I'm perfectly fine with an informed patient declining anything they want, and have many clients who've not wanted this or that and it's no big deal. I see my role as offering services and expertise, and my patients choose them or not. I assume that's why people hire me - not that they are feeling like they need to protect themselves from me.
I love teens and preteens, actually, and really enjoy seeing them. I like their honesty and enthusiasm. I think the fact that I genuinely enjoy my young patients is obvious to them, as that is one area of my practice that is always booming as young folks send their friends to me. I see visits with young folks not as an opportunity to coerce them into a bunch of stuff or prepare them to be sheeple, but as the chance to start a good working relationship together so if they need me for anything more personal/serious down the road they are comfortable coming back and know I will be respectful and helpful. That's all I'm trying to do.
As for the OP, good for you for working it out in a way respectful to this young man. Perhaps the doc can explain to him at a time when he is not needing any exam why he looks for hernias in young guys and help him feel more at ease in the future. And if he's never more at ease, at least he'll know what exactly he's declining.