If you find that club members are being charged green fees during booking this is most likely due to the membership category not having the correct playing rights assigned. 

You can check this by clicking on Settings > Categories, and then selecting the appropriate membership category.

This will show you the profile of the selected membership category. If you scroll down on this page you'll see the Category Limits section which is where you enable the specific playing rights:

If these aren't set then the system will assume the member has no playing rights and will charge them a Green Fee.