No big deal. Seems like maybe you overreacted a bit? All sounds normal. Hopefully he doesn't think touching himself is bad now - it's not.
Allow your son to be naked arond the house more often (supervised of course). You'll be surprised how quickly he would grow out of it.
Why would a boy touching his penis be considered un-natural? Your son is 5 years old so I'm going to assume he stands when he pees. How does he manage that without touching himself, must be pretty messy.
Come on now, for boys thier reproductive organs are right out there for all to see. Doesn't it make sense that at one point they are going to look down and think "Well hello there and what is this?" My brother-in-law as a 3 yr old got his stuck in a wind up toy because after putting it against the end of his nose he thought, well there's something else that sticks out from my body, wonder what would happen......
I have 2 little girls and they have touched themselves. It is shocking and uncomfortable. I have told my older girl who is almost 5 that there is a reason that it is called her privates. That when you want to touch it you do it in private. She has long since stopped doing it infront of anyone, if at all. She would do it while watching TV. I guess she'd rather watch TV.
I do not believ that young children instictivley know about these things, swinging his penis around is a joke amongst some males I believe it is a learned behavior,they always say no,or dont know, I would check out if he could have seen this behavior anywhere, moms want to hear the best but it is good to be aware of what is going on around you.
I agree with mylittlelammy. He is just curious. He knows it is a private thing by hiding. But he shouldn't be made to feel ashamed. Tell him he just needs to keep it where no one can see him doing it. Under the covers is fine. But keep a watch on him to see if he is into any other activity of exploration. Since he didn't confess, I assume he already feels ashamed. Try and keep the communcation going by treating it as a matter of fact.
I think your child just might be curious. Sometimes my child does things that I don't understand either and it's not that anyone has taught him these things but his own learning and understanding. Just yesterday after his bath he decided to swing his penis around just because he could and sometimes I do see him touching himself but I don't think anything of it. If you are still worried please call your family pediatrician. I hope this helps you!