The answer "who pays for it" is that as all the data is going over Broadband and wi fi and mobile phone networks we are all paying for it when we sign up for Broadband or mobile data on our phones.
The companies we pay (Virgin, BT, Vodaphone etc) put in the various networks (broadband cables, mobile phone masts etc) using the money we give them to use their services.
The actual apps like Whatsapp and Skype do make some money as Buenchico says, from things we sign up for.
But nowadays having customers "signed up" is king. Once you have customers signed up (to any service) you can advertise to them and that makes a lot of money.
Look at Facebook, it costs nothing to use, but billions use it all over the world, because they can advertise to us while using it.
Over 1 billion people use WhatsApp yet it has never made a profit.
Facebook bought it for 19 BILLION dollars in 2014 which is not bad for a product that was only released in 2009 and never made a profit.
One way to get rich quickly is to "invent" a popular program or smartphone app and sell it to Microsoft, Google, Facebook etc.