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You might have forgotten to install the dev package of iptables. In Debian/Ubuntu, it's called libxtables-dev.
A bunch of people doesn't want iptables, so it's an optional dependency. If you have it installed, Jool's makefiles compile with iptables. If not, iptables is excluded automatically.
You can tell whether iptables is being excluded by finding the "checking for xtables..." line during ./configure:
$ ./configure | grep "checking for xtables"
checking for xtables...yes
"yes" means iptables dev was found. "no" means it wasn't found.
Why does my system support iptables and I follow the tutorial to install jool only to be told that natfilter is the only framework
root@mqh:/usr/lib# jool_siit instance add "example" --iptables --pool6 2001:db8::/96
Error: Netfilter is the only available instance framework.
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