In the dark ages of my career, when I commuted for about 2 hours in each direction, I had to leave home at 5:30 in the morning to catch a 6am train to be sure that I would be at work by 8. I would put foundation and powder on at home, nap for the first half hour of the train ride and then put on eye makeup (usually just liner and mascara), blush and lipstick on the train.
It was just too damn early to care what people thought. Most of the other passengers were asleep anyway, and most of those who weren't asleep were reading newspapers.
Having said that, there were men who would clip their toenails (yes, toenails!!!) on the train. By those standards, applying a little eyeliner and lippie is pretty tame.