It's instructive to actually have a look at a block in blockexplorer - here is the most recent one, as of writing:
http://blockexplorer.com/block/0000000000000224615e7dc4006fcc1baec60b7cc3fa102332575ef53d2b8be0Note the list of transactions embedded in the block, and that the first transaction has no "from" address, this is the miner receiving the block generation subsidy plus the total value of transaction fees for all the other transactions in the table. For the other transactions, for any with fees you should find that the sum of the outputs, plus the fee, is equal to the sum of the inputs. That is where the money comes from, and if it didn't add up the transaction would have been rejected as malformed way before being included in a block.