Men holding doors for women and calling a woman "miss" or "ma'am" can often be mistaken for flirting. Being nice isn't necessarily flirting. It's just being nice. Perhaps our society is so informal now that true manners are absent in everyday life. Sometimes, it's just the right thing to do when someone is nice when that person isn't flirting whatsoever.
No, manners are not often mistaken for flirtation in today's society, because America is still a very conservative nation. We are a nation of people that are helpful, and people that are polite. Most people know that this is not necessarily to be interpreted as flirtation. Most people are happy to just help each other.