That is the issue. If you enjoy a beer on the train on the ride home and your blood alcohol level is below the legal limit for where you're driving, then you're good.
States with Open Container Laws do make the distinction of a driver who is working, like a limo or taxi driver, being exempt from the law, and types of vehicles like a motor home with open containers being ok in the living area. And police officers can generally tell if a can is fresh or old, and whether a driver is intoxicated, etc.
But nobody can have an open container in a regular car, otherwise. If you were to take a bottle of wine home from a restaurant, say, it would either need to be in the trunk, or in the case of an SUV, way in the back, re-corked and bagged, with receipt showing, from the restaurant.
http://www.boston.com/news/local/articles/2010/01/17/clarifying_what_constitutes_an_open_container/