ShapeShift does not charge a specific fee. Instead, we offer an exchange rate for each coin which changes every 30 seconds with market conditions. We try to earn revenue by offering a profitable exchange rate, and typically we earn in the range of 0.5% (50 basis points). You receive exactly what the exchange rate shows, there is no additional fee (except the tiny miner fee).
So as an example of how you would calculate the following posted "Instant Rate"
In this example, the Instant Rate posted is 1 bitcoin = 40.85042657 Ether. You would calculate the amount you would receive by taking the amount of bitcoin you plan on depositing- let's say for this example we are depositing .5 BTC- and multiplying it by 40.85042657 Ether.
.5 x 40.85042657= 2.42521328
The only fee that would be removed after doing this calculation is the Ether miner fee. You can see this in the above image on the right-hand side posted as 0.01 ETH.
So the final amount of Ether you would receive would be:
.5 x 40.85042657= 2.42521328 - 0.01= 2.41521328 ETH