Tokyo's station serves 3000 trains daily and some 415K passengers per day as of 2013.
The Chinese high-speed rail system also deals with similar levels of passenger traffic. Shanghai's Hongqiao station for instance has no less than 30 tracks, can hold 10K passengers at the same time, and comfortably serves an average of 210K passengers per day (much more on holidays), and it is only one of a few railway stations serving the area.
Trains scale well if you do them right. Technology has come a long way.