Transaction fees are a service charge paid to the miners who record the Bitcoin ledger. The services provided by miners are transaction validation, storage of the ledger and the construction and security of the Bitcoin network.
Every Bitcoin transaction transfers one or more satoshis to one or more recipients. The difference between the amount being spent from previous outputs and the amount being sent to new outputs is the transaction fee (which must be zero or more).
Bitcoin's design makes it easy and efficient for the sending party to specify how much fee to pay however it is theoretically possible for a merchant to pay the mining fees on behalf of their customers as an incentive to use their service. Services that make this possible have been proposed.
When a miner creates a block template, they are entitled to specify where the fees paid by the transactions in that block proposal should be sent. If the proposal results in a valid block that becomes a part of the Block chain, the full block reward including the transaction fees and the block subsidy will be sent to the specified recipient. Miners are forced to wait 100 blocks before they can use coins received in a Coinbase transaction.
Loss of fees
If a valid block awards its finder less than the available fees plus the Block subsidy, the Satoshis which are not collected are permanently destroyed. This has happened on more than 1,000 occasions in Bitcoin's history reducing the token supply by over 50 Bitcoins.
An example of this can be seen in block 164246 where the miner lost 1.76 Bitcoins by not claiming the fees.
The Bitcoin Fee Market
A default minimum fee is usually needed for a transaction to be propagated across the network and mined into a block however a market has arisen offering discounted transactions for bulk generators. The upcoming Merchant API package will give miners a means by which to interface with regular users and to offer their own unique pricing on a per-node basis. User wallets will be able to make use of this service to present users with fee rates that present estimated 'time to confirmation' giving them flexibility to choose lower fees for larger or less important transactions, without having to worry about those transactions failing to propagate.
This article contains a deeper perspective on this aspect of Bitcoin fees.