Because the microbus between Aswan and Kom Ombo takes the road along the Nile rather than the desert highway, it should be possible to take a microbus to/from Aswan (LE25). At the time of writing, however, foreigners were not allowed to travel on microbuses.
The easiest way to visit the Temple of Kom Ombo is to come on a tour or by private taxi. Hiring a driver from Luxor for a day trip taking in both Edfu and Kom Ombo will cost LE900 to LE1200; moving on to Aswan instead of returning to Luxor will cost between LE900 and LE1200. A private taxi from Aswan will cost LE400 to LE500.
Trains are an option, but the station is 3.5km from the temple (take a taxi).