Fees applied to transaction go to support the networks that run the coin/token - so, for instance, every standard (non-contract) ETH transaction currently applies a fee of .000441 ETH. This fee does not go to us; it goes to reward miners (thereby ensuring that the transaction is logged into the blockchain in a timely fashion) and support the Ethereum network itself. Note that transactions that interact with a contract address will be more costly.
The same is true of Bitcoin - BTC fees applied go to the Bitcoin network. The difference is that the BTC fees applied are dynamic - they are subject to go up or down based on the state of the network. Jaxx lets you specify between three different fee options depending on whether your transaction is time-sensitive or not (as the lower fee may face a longer confirmation period).
As newer coins are implemented, each coin is subjected to their own transaction fee that goes to their respected networks.