I was going through this article on iptables and there the author said that:
It's important to turn off ECN (explicit congestion notification) so that Internet communications will work properly.
Why do we need to disable the ECN?
There used to be a lot of broken routers out there that would drop any packets with the ECN bits set. I remember trying it and experiencing this personally. This site gives you a taste of how things used to be, particularly the "8% of the internet unreachable!" link. It's of roughly the same vintage as the article you linked; as Mat pointed out, the article describes Linux 2.4, and 2.6 was released in 2003...
Even now, years later, I wouldn't be too surprised to hear of broken routers still out there given that ECN still ships disabled on major platforms (see wikipedia). So you could turn on ECN, forget about it entirely, and later be unable to visit some site without knowing why.