The Upper Egypt Bus Co, at the bus station opposite the train station, runs regular services to Cairo via the Red Sea, Hurghada and Suez.
At the time of writing, foreigners were not allowed to use microbus services. When this changes, from the station, 1km inland from the bridge, you will be able to get south to Luxor and Aswan, east to Hurghada, Marsa Alam and Suez, and north to Nag Hamadi, Sohag and Asyut.
All main north–south trains stop at Qena. There are 1st-/2nd-class air-con trains to Luxor (from LE27/19, 40 minutes) and trains to Al Balyana (2nd/3rd class LE18/12, two hours).