While I agree - who pays? It costs a bundle. To go with the engine transponders for a minute - they add a couple hundred thousand quid to the cost of an engine over it's life span. Rolls swallows the cost, since they are both optional and only normally fitted to the first 20 engines in a new series (new is relative).
Some airlines do have the aircraft transmit a lot of data, and they gladly pay for it because it helps with maintenance, reliability, and improves dispatch rates.
Boeing pays for it on new aircraft (not as in newly built, but a new model such as the 787 or a new model of an existing version) and as mentioned, the engine manufacturers pay for it as well under some circumstances.
But most of that is simply numbers, easy data to transmit and store compared to transmitting every single a word spoken in the cockpit and every single bit of operational data, even beyond what the FDR records.