To minimise transport time to the terminal for early morning departures or late arrivals, stay close to the airport.
Hotels near the terminal
There are 2 hotels right next to the terminals at Lyon Airport, with prices around 120 eur per night.
Both hotels can be found opposite the terminals with a walking distance of up to 5 minutes.
Lower prices from about 90 eur will be offered by 2 other hotels about 1,5 km from the terminal. Both offer a free transfer to/from the airport.
Hotels in the centre of Lyon
The airport is not far from the city centre, so you can easily stay right in the city even for early morning departures. Regular prices for classic 3* hotels start at 100 eur.
A little further afield, you can stay quite cheaply at the Premiere Classe hotel - it's a couple of stops from the airport on the 47 line (the other way from the city).