It seems to come down to the fact that people are often comfortable with one of two styles:
1) Know nothing, and poke at it until works. If it quits working, poke at it until it works again. Fill in gaps as necessary along the way. I think in psychology, this is called the procedural learning style. Step-by-step. If it breaks, learn a new procedure.
2) Understand how all the essential cogs turn, so an educated guess can be made at how to start from scratch, and how to anticipate, or at least fix errors that come up. This is the intuitive learning style. If it breaks, find out why, and consider how to apply this in the future.
I'm in the second camp. Using an IDE is terrifying for me, because so much stuff "just happens", which means I don't know exactly what actually ended up on the chip, or really how it got there. I know I wrote some code, and it seems to be doing more or less the right thing, but I can't be confident that I did everything correctly. In which case, there's a good chance a different IC or a particular interrupt or a change in clock frequency could bring the whole house of cards down. Not great for confidence.
In my line of work, I've noticed most people seem to be Type 1s. They just go about their job and do what they've been told (or learned) to do. There isn't much thought about whether what they've been told is always, only sometimes, or not at all correct. If they do what they're told but a process fails, well... *shrug* I followed the procedure I was given, didn't I?
Now, once you know what happens under the hood, an IDE can automate all of that tedious stuff and make your life easier. Great! But I agree wholeheartedly that, while you're learning, it's a distraction and makes it 10x harder to understand where and why something failed.