There are no direct flights between Faro and Malaga or between Faro and airports in mainland Spain. To fly you would have to route via Lisbon and Madrid as the TAP/Air Portugal direct flights are expensive.
The only public transport route between Faro and Malaga is by bus.
Alsa.es have a daily departure as follows:
FARO dept: 01:45
MALAGA arr: 08:45
Current Price: €40.00
It is also possible to take the twice daily DAMAS/EVA buses from Faro to Seville and then get another bus to Malaga.
For more information see Cubsur's very useful website here:
http://thomasallen.home.sapo.pt/travel/001.htm
