RE: Did you start shooting the wrong way?
I was started the proper way with shotguns. First a .410 single shot, then a 20gauge single shot, then a 20 gauge pump, then finally a 12 guage pump. I never even think twice about shotgun recoil.
Rifles are a different story. I shot my BB gun and open-sight, single-shot 22's all of the time growing up. I was deadly with open sights. Still am. But when it came time to start big game hunting, the hardest recoiling gun I had ever shot was a 20 guage, and I had never used a scope. My dad went out and bought a Remington Model 7 youth rifle in 7mm-08 and took me out once to shoot it. It was a really light rifle and it didn't have any sort of kick pad. At the time, we still didn't have a scope mounted on it. The first shot caught me totally off-guard. The sharp kick of the rifle was much different than the push of my shotgun, and that light little rifle bucked pretty good.
Fast forward to my first hunt. In the few months before elk season, my dad had a scope put on the rifle and he had a friend sight it in since he didn't have time. He threw the rifle in my hand and we headed up to the mountains on a late season elk hunt. As soon as we hiked into our spot, elk were everywhere, but they were all moving. A band of cows ran 50 yards in front of me, but I couldn't pick them up in my scope because I had never used a scope before. A few hours later we got about 300 yards away from a herd of about 400 cows that were filtering through the trees across the draw, but I didn't feel even remotely comfortable taking the shot. I hadn't ever even shot at 100 yards. Later that day we got up on some elk bedded in the timber and I shot at a cow that was only about 40 yards away. I don't think I even came close. The experience shattered my confidence.
The next year I went on my first antelope hunt. I still hadn't hardly ever shot the gun. To make a long story short, I missed the biggest antelope that I have ever had my cross hairs on to this day five or six times, then proceded to shoot nearly two boxes of ammo before I shot a puny little 12" buck. My confidence was thoroughly shot.
I usually don't have any issue with flinching, but to this day I always second guesse my shooting ability. The thought that I might miss is always in the back of my head. When I sight my rifles in I always think to myself "what if I wasn't shooting properly and my gun isn't really sighted in?". But as time goes on and I shoot more, I doubt myself less and less.
When I have kids of my own, they'll learn to shoot shotguns as I did, but rifles will be a different story. They'll start with BB guns, move to open-sight single-shot .22's, then to scoped .22's, then to my heavy barreled .243 with slightly reduced loads. Eventually they'll graduate to full-power .243 loads, then a 7mm-08, and finally whatever large caliber rifle they choose.