Grant, thank you for sharing your story and I am very sorry for the loss of your father. I hope you had a good relationship with him. Mine grew to a great relationship with my father, once I got to an age where I realized I didn't know everything and my dad became smarter and smarter.

My father has been gone for 24 years now and I still miss him daily. Some days much more than others and I know he would be proud of his grandson and the great young man he has turned into and I wish he could see his great-grandchildren. He became softer as he aged and maybe that is why I had a better relationship with him than my older siblings did.
Looking back, I think that bond between my son and I was strengthened immensely as I watched him, talked to him and held his little hand all through the incubator for those first couple of months. I can totally understand your ex-wife wanting to wrap him up in a bubble to protect him as I feel I was the same way. I developed a strong situational awareness and practiced risk avoidance greatly with our son. There were things I used to do as a child growing up on a farm that in no way on God's green earth I would allow him to do.
Yes, we did a lot of motorsports activities, but him being safe was always the first and foremost point of concern. Even when he was old enough to ride a quad and snowmobile by himself and even with proper training, there were certain times of day we stayed off the mountain due to other people's patterns. We avoided certain trails at certain times of the day as masses of people were heading back to their vehicles in the parking lots. We took out of the way routes to avoid those high-speed idiots who thought the trails were their personal racetracks, etc.
When my son expressed the desire to start riding a motorcycle in high school, I immediately put my foot down and said no. My wife explained that I was being a bit of a hypocrite because I had been buying, building and riding motorcycles for the better part of our marriage even though my father was not pleased with my choice. I conceded under one condition, that he would take a proper riding course and learn from someone other than myself because I know how kids are when it comes from learning everything from dad. A non-biased or third party often times gets through better than a father does. He agreed but wanted me to take the course with him. I agreed.
When we would go on rides, I often times explained risk avoidance and just not putting oneself into certain situations when it wasn't necessary. Things like watching the front tires of cars when pulling out of parking lots to reveal signs of a car preparing to move, avoiding certain traffic lights or intersections at certain times of days, making a right hand turn and going around the block or to a light vs. trying to cross traffic and make a left-hand turn. All of these things were done to protect him and keep him safe. I have always felt like we fought so hard to get him here and the good Lord has blessed him for a reason, then it was up to me to make sure it wasn't for not.
I'm sure I have been overprotective, but I just hope he knows it was all for his benefit, but also because I'm selfish and I don't think I could live with myself if anything happened to him, especially doing something I introduced him to or allowed him to do.
The downside to that is now I feel the same way about my grandchildren; I want to wrap them up in bubble wrap and protect them from the world we live in. I'm sure that's not a healthy behavior on my part though, the stress becomes overwhelming at times.