The other airline you may try for domestic travel within Turkey is Atlasjet Airline. The owners of this low cost airline are two tour operators, Estur and Oger Tours who started this to fly tourists from Europe to Turkey. Today it has expanded enough to fly other domestic travelers and pose a competition to the traditional carriers like Turkish Airlines and Onur.
Like Fly Air, you will find the fares low, but airport transfers may have to be paid extra, adding to the total cost. Reservations may be made online. You may also find some travel agents booking tickets for Atlasjet, but they are generally reluctant to book for Atlasjet as the commissions received from the airlines is very low.