To be clear, Skype has 3 different modes of operation:
Skype-to-Skype.
Any Skype user can always make an unlimited number and duration of calls to any other Skype user anywhere in the world. This does not affect your cellular airtime, and there is no other fee.
SkypeOut.
You can use your Skype account to call any public telephone number in the world for low, low rates. The person receiving SkypeOut calls will pay their own incoming call rate, whatever that may be. This also does not affect your cellular airtime at all. Skype will require you to prepay into a separate account (not associated with Apple, AT&T, or any other cellular carrier) to cover the cost of these calls.
SkypeIn.
You can use your Skype account to receive calls from any public telephone. This also does not affect your cellular airtime at all. You do not pay any per-minute fee for the incoming calls. However, you do pay a monthly, quarterly, or yearly fee to Skype to maintain this incoming number, which is separate from your iPhone's regular phone number. The person calling you will pay their normal rate, whatever it may be, to call the area code in which your SkypeIn number is registered. You cannot register your SkypeIn number to be located within some countries.