The main reason why car hire companies ask for flight numbers is because majority of the suppliers will allocate you a vehicle before you arrive at the counter to pick it up. The incoming Flight Number indicates to the rental car companies what time your flight is estimated to arrive and the terminal of arrival so your booked vehicle is ready for you to collect.
By providing your flight information, rental agencies become aware of and up to date with your flight's arrival time and any delays which may transpire. In addition, if your flight has been delayed or cancelled, suppliers then know to keep your reservation until the delayed time, and will not cancel your booking because of a "no show".
Please don't worry about giving your flight number to a reputable car rental service. After all, the ultimate reason they ask for your flight number is because they want to provide you the best customer service possible.
Click here to learn more about the process of Airport Car Rental in Australia.