The train argument can always be used. After a London engagement, Charles and Camilla can stay at CH and take the train the next day to whatever estate he's going to or his next function but they don't. All senior royals have at least two residences.
The cost of leasing and using the helicopter is factored into the budget every year. It's part of what the royal household does.
It's not for just emergencies, it's not just for the Queen. There is absolutely no abuse in taking a helicopter between Norfolk and London, especially when you're the 2nd in line to the throne.
William and Catherine use British Airways when travelling internationally, and Charles charters private jets. So it's all relative I suppose.