Yep, this is it.
What you're actually getting at here is the fact that judgment and airmanship cannot be taught in a classroom. Since it takes experience to actually develop judgment, there are two ways to ensure inexperienced pilots make safe decisions: constructing an environment with a lot of rules where pilots don't have to use any actual judgment (just follow the rules), and modeling good judgment and decisionmaking as an instructor that your students can emulate.
In places like a university, a 141 school, or the military, both can be done. In the 'wild west' of the Part 61 world, it is difficult to have a tight rules set, so an instructor's demonstration of making good and bad choices is going to be the most influential piece. If the instructor is nervous or unsure of themselves in the tasks they're performing, then their student will follow and likewise be unsure. Just as importantly, if the instructor is calm and confident when something new or "dangerous" (as perceived by the student) is performed, the student has the greatest opportunity to NOT be afraid of it.
I agree with you 100% Hacker. Some of us learn to fly many moons ago in which 141 schools were around but not widespread(1977). I went the part 61 route because the program wasn't as expensive as the part 141 program. The FBO I learn to fly at had POI's who were not entirely familiar with all the protocol required of part 141. Once all of my training was completed under part 61 in which took me a long time, I was able to advance to part 135 cargo, part 91/135 charter/business jets. Part 135 was where I learn all about ice, didn't care about crosswinds, flying approaches down to 1/2 a mile, 1800RVR, and 1600RVR. Part 121 regional, and then part 121 logistics company. No military experience! Pilots will generally learn as they go along and if they live through their mistakes, I am sure every pilot has a story to tell.