Turkey is a big country for travel. There are enought options to travel in Turkey. Some options are Travelling by local bus, Travel by private minibuses and Domestic flights can be a choice for you.
Local buses has very good bus link around Turkey. you have a chance to catch bus from any cities to another if you make head booking
Private minibus rental will be another choice for you and your family. especially if you are mini group of family this way travel will be enjoyable and more reasonable.
Turkey has also flights link between the touristic destiiinations. Mainly they are via istanbul or via ankara so sometime it is not a way travellers choice.
Yes ofcourse you can travel by bus and flight. You can use flight for long destinations and bus for short destination. You can combile 2 transportation ways.
Also you can combine flight and private minibus travel that will be possible and you will enjoy it.
How ever there is one more choice but this choice may not be possible in many destinations. Possible destination for now is istanbul to Gallipoli peninsula this is tour bus and easiest way to travel in Turkey