We dance around what we would really like to say in the hopes that the other person in the conversation understands what we mean. We change our language to fit the situation we are in. We use our language to manipulate people, and, ultimately, to get what we want.
You are right, people do use a lot of context when conversation is going on based on tone and wording. We use a lot of previous experience to figure out exactly what others are trying to say. I think this can also become a big issue when two people who do not know each other very well share a conversation. One person could say something completely harmless, but in the other's experience it is taken as an insult.
It makes me happy to know that linguists will use my numerous speech errors to judge me for my performance and not my competence. At least let me keep some of my dignity.(Emily Callan)
I think that this article really went back to something that was brought up earlier, which is politeness. Perhaps the reason people tiptoe so much is to make themselves seem more friendly and approachable. Maybe another reason is habit and inheritance. One generation somewhere in the family started speaking indirectly so as not to seem rude, then their kids learned it and their kids, and so on.