It seems you are very new to futures.

Please be careful. New traders can lose a lot of money in derivatives trades.

1. Yes, the brokerage for futures is calculated in the same way as for stocks.

The rates are comparable to intraday rates for stocks in the cash market.

e.g. These are the rates charged by Kotak Securities:

Low Brokerage | Brokerage Charges | Broking Charges - Kotak Securities
2. "Cost of carry" is not a real cost, but an implied cost.

Usually prices of futures trade at a premium to the prices of underlying securities.

The difference between the price of futures and the price of the underlying is the "cost of carry".

The cost of carry on NSE's site is

annualized and expressed as

percentage of price of the underlying security.

(I have simplified the cost of carry. NSE's site uses compound interest formula to calculate the cost of carry).

3. (Initial Margin + MTM loss) will be deducted.

Whenever you take a position in futures market, a margin amount is blocked.

You can read more about margins here:

http://www.nseindia.com/invest/resources/download/futidx_invguide.pdf
The initial margin serves as a security deposit, which in turn the broker has to pay to the exchange. Your positions in the futures market will be revalued or "marked-to-market" everyday. This is done by the exchange to assess the value of your positions on a daily basis. If the market value of your position shows a loss, then you would be required to pay the difference. Similarly, in case your position has gained in value, you will be paid the profit amount.