I think its a combination of the two things as well. Internal pull ups are not obvious and need explanation, but the code that enables them at the moment tends to look like a coding error to a beginner rather than something that has a clear purpose even if you are not sure what - without a comment you simply wouldn't know by looking at the code - alot of other arduino syntax you can guess what it is doing and have a good chance of being close.
For someone who is in a class they get the explanation, and in time it often makes sense, but for someone who is working alone and using the documentation it may be harder. The pages explaining pullups are heavy on text with no diagrams or pictures, so look more intimidating than the pages that they may have been looking at that go with the example sketches.