The rc.flush-iptables.txt script should not really be called a script in itself. The rc.flush-iptables.txt script will reset and flush all your tables and chains. The script starts by setting the default policies to ACCEPT on the INPUT, OUTPUT and FORWARD chains of the filter table. After this we reset the default policies of the PREROUTING, POSTROUTING and OUTPUT chains of the nat table. We do this first so we won't have to bother about closed connections and packets not getting through. This script is intended for actually setting up and troubleshooting your firewall, and hence we only care about opening the whole thing up and resetting it to default values.
After this we flush all chains first in the filter table and then in the NAT table. This way we know there are no redundant rules lying around anywhere. When all of this is done, we jump down to the next section where we erase all the user specified chains in the NAT and filter tables. When this step is done, we consider the script done. You may consider adding rules to flush your mangle table if you use it.
One final word on this issue. Certain people have mailed me asking me to put this script into the original rc.firewall script using Red Hat Linux syntax where you type something like rc.firewall start and the script starts. However, I will not do that since this is a tutorial and should be used as a place to fetch ideas mainly and it shouldn't be filled up with shell scripts and strange syntax. Adding shell script syntax and other things makes the script harder to read as far as I am concerned and the tutorial was written with readability in mind and will continue being so.