I think it's because in English culture it's only really used now in extremely formal scenarios where you're talking to someone in a position of great power, occasionally in very traditional customer service, or in more formal schools for pupils to refer to male teachers.
When an American says "sir" to me, I know I'm not in any of those positions, so it comes across as parody of those – highlighting the fact that I am not actually in the position of power, or that I am not a highly valued customer. In that way it's sarcastic, and it can imply that I'm actually imposing on the other person and taking that position of power, which as I'm not, therefore comes across as passive aggressive in a way.
If an American asked me to do something and I said "yes Mr President", arguably referring to the highest status in the culture, I expect it would be taken as sarcastic or rude, not polite, because the person is not in fact the president. That's sort of how I see it, but maybe this analogy doesn't work.
When an American says "sir" to me, I know I'm not in any of those positions, so it comes across as parody of those – highlighting the fact that I am not actually in the position of power, or that I am not a highly valued customer. In that way it's sarcastic, and it can imply that I'm actually imposing on the other person and taking that position of power, which as I'm not, therefore comes across as passive aggressive in a way.
If an American asked me to do something and I said "yes Mr President", arguably referring to the highest status in the culture, I expect it would be taken as sarcastic or rude, not polite, because the person is not in fact the president. That's sort of how I see it, but maybe this analogy doesn't work.