Zebpay have their own fee structure and it is also more or less same as any other exchanges.
In terms of fees zebpay does not collect any amount. They directly have the spread between buy/sell. And that difference is their profit. Well this difference is so much that sometimes its more than 6000 per btc. Almost 7-10% around 1 btc.
While fees charged by others is around 0.3 - 1.15 %
This should not be the case. Check out bitcoinrates.in clearly it is 0% there. For example if you sold 1 btc @ 60000, you will get 60000 and nothing less than that. May be that 40 Rs is some withdrawal charges you may be saying about if they have so.
Zebpay has two options Trade bitcoin and Buy/Sell bitcoin.
Buying and selling bitcoin has no additional fee because they already selling at high price.