I'm glad I came across this post. I had first started modifying the iptables file directly, then found a few sites saying that this was real bad juju. I'd take the opinions of AT Linux gurus over random google sites any day of the week 😉
It's not bad juju. That's how I've always done it because that's the way I learned, and that was from a Red Hat class. Some people might not like directly editing the file because if you make a mistake and somehow lock yourself out (if you're connecting remotely) then you're screwed, because the iptables file obviously persists across reboot.
If you use either method correctly then what is the difference?