The cost per transaction is incredibly cheap, if you don't include the cost!
The 12.5 BTC per block is given to the miners as incentive to keep mining and verifying the transactions. Also, the cost of mining rapidly converges on 1 BTC per 1 BTC mined (both theoretically and in practice). Thus, that is actually the cost for the bitcoin system to process transactions.
(Ignoring for the moment the BIP66 incident and the discovery that many miners were literally not bothering to actually verify the previous block, in order to save a few seconds per block.)