On most airplanes with cellular and Wi-Fi capabilities, the ability to
make mobile phone calls is technically disabled and passengers are
prohibited from using the Wi-Fi service to make VoIP calls using
services like Skype.
Small point - Skype is not VoIP (in the technical sense). It uses its own proprietary protocol.
It is not airlines that prohibit voip calls, but its the provider that is being used and the bandwidth that is available for the flight.
In some areas, it may be blocked by the government. For example, in Saudi Arabia - WhatsApp (voice) is blocked, facebook calling doesn't work. In UAE, Skype is regulated as well.
Now, as to why the airlines provide telephones - these are because they are fitted to the seats, and its very rare for an airline to replace the seats in an airplane (its a significant upgrade) and its cheaper to install the wifi and cellular connectivity. So if you are sitting in an airplane with a traditional headset, it is likely an older aircraft.
Most modern aircraft seating eschews the telephone in favor of the onboard microcell (a mini cellular tower) in the airplane and WiFi.
The cabin crew has the ability to turn on and off the wifi and cellular service. It is usually turned off during the critical phases of flight.
Practically speaking, I used WhatsApp voice (which is more similar to Skype than a traditional VoIP application) on board the Emirates A380 without issue - although it did take a while for the device to login to the wifi after the initial connection.
The onboard cellular service (the new one), is billed by your carrier as international roaming. The older calling service (where you used to swipe your credit card into the headset) is billed at a premium by the service provider for that service.