We went from Marsa Alam to Luxor by public transport, and it took nearly 7 hours in total: Shared Peugeot from the hotel to Marsa Alam (10 LE p/p), minibus to Edfu (20 LE p/p), minibus to Luxor (15 LE p/p). (Needs some haggling, and even so you sometimes end up paying more than the official, posted price). Especially the last leg was very slow because of the traffic and the bad road. In general, it is better to travel in the morning – you may have trouble finding a minibus going in the afternoon on the lesser-travelled road (i.e. back through the desert). Also, don't travel on Fridays.
You should consider making it two nights in Luxor (you can get a room with bathroom from about 120 LE), which would give you a full day for the West Bank sights plus the afternoon for Karnak, Luxor Temple and one of the museums. Alternatively, even a taxi for some or part of the distance might be cheaper than the tour (especially for more than one person).
Photos, hotel reports and texts from our Egypt trips: http://westwards.typepad.com/westwards/egypt/