Where to wear the Glengarry??

[Nanook]

I'm sorry but that's hogwash. Removing one's hat when it is appropriate is a sign of courtesy and respect.

For you its a form of expressing "courtesy" and "respect". To others its a sign of submission, surrender and others still a act of meekness, humility or..

How did we get to the point where we consider bad manners to be "personal preference"? Manners are about respect for others.

That's right and NOT suggesting that others should remove their hats to conform to your cultural traditions and views. Even within many Christian denominations were the male of the flock are forbidden to cover their heads--- hats are reserved to the ordinated (leaders) men--- women are traditionally expected to wear head coverings (in the United States among some of the churches in the South its tradition for black women not just cover their heads with kerchiefs but to wear extremely ornate hats).

. A man will uncover in private spaces (homes, personal office etc.). A restaurant is considered private space because people are eating so a man will be uncovered at all times. Is that really difficult.

Not really. In many schools boys that normally don't wear hats are expected to wear hats especially during meals. There are rules about local custom and in areas where its local custom not to wear a hat on the streets (public) its acceptable that one go without a head covering but in closed spaces its time to put the hat on! I know many men and boys that only cover their heads indoors--- hat in pocket and plonked onto their heads when they enter closed buildings (or away from the public eye). Head coverings in public can also be very political. In many places some forms of hats are illegal. A Songkok or Kapiah in one place can mean prison in another. A gansta too can't just remove his bandanna as its part of his colours yet the same colours can get him arrested in large parts of the U.S. that have initiated anti-gang legislation (where some forms of self-inflicted body mutilations are sufficient evidence to be arrested as a member).

I wear hats, so do both my boys and the oldest (7) knows the basic rules. He has asked my why someone is wearing a hat at the wrong time several times.

Why do you assume the "wrong time". Perhaps its was the "right time"?
In the "big picture" from a global perspective the feeling that removing ones hat is a sign of "courtesy and respect" is perhaps even a minority view..... Your view but not everyones.