Everybody is gaming the system, be it web masters that do link exchanges, be it paid posters, be it selling links, referrals, etc. Footer links are no different than that.
By promoting nofollow links he's trying to convince people that completely fair system is possible. Its like trying to make communism work - good idea on paper, impossible to implement in reality. We don't live in utopian world. Good websites are not hobbies, they are there to make money for someone. Its business. Everyone wants to get some edge over competitors.
If links in footer would not be followed by search engines because someone at Google thinks those links are unnatural, they should do the same with all other links that could potentially be unnatural - signatures, referrals, link exchanges, paid posters, spam, etc... Then they'd need to be able to tell apart natural links from unnatural, which is impossible, so safest bet is to make all external links on all websites nofollow. Otherwise someone would be able to game the system.
Links in footer are there to promote someone's website in order to sell products. If links won't work, author would have to find revenue elsewhere. There would be much less incentive to release stuff for free and commercial stuff would cost more.
So whole idea of nofollow links is counter productive for everyone.