I think you are misunderstanding the word confidence in the sense that Kahneman is using it. One can also be over confident in one's notion that the girl wouldn't want to talk to you, the raise is unjustified, the customer doesn't want the product, and the oppressor is unbeatable. By your examples, you seem to be associating it with self-esteem, whereas in Kahneman's case it's more of an epistemological issue.
agreed - what the article is trying to say (i think) is that human's are too confident about first intuition (system 1), their "gut feelings" and because of that they are affected by serious problems like the base-rate fallacy, etc
