The article seems to argue that because there is no perfect solution to spam (i.e. spammers will still want their links on SO even if they are nofollowed), then there is no point in marginally reducing the incentive to spam.
I think the point is myopic. Human moderators will eventually clean up spam, but Google is freakishly fast at indexing things like StackOverflow. Omitting rel=nofollow would mean that SO ends up lending linkjuice to spammers at least some of the time, thereby providing spammers with incentive to relentless spam even if their spam is cleaned up by humans.
My general rule of thumb is "any content that comes from untrusted users gets a nofollow stamp". It's "XSS prevention" for your pagerank.
When I say "trusted users", I mean "people who have the product's interests before their own". I don't think this applies to users, even high-reptuation users.
Arguably, it eliminates incentive to link to anything except the most useful resource. I have >11k reputation on SO, and I'll easily admit that I'd be tempted to link to my blog or whatnot for an answer whenever I could wedge it in, if I could siphon off some of SO's linkjuice. I'm not interested in spamming or anything, but that's how the game is played; SO has such a massive amount of clout with Google that any non-nofollow links from it confer an awful lot of weight.
By just nofollowing everything, they disincentivize people from even being tempted to game the system and promote their own stuff, even if it were done in a helpful way. Instead, I am incentivized to provide the most useful, comprehensive link I can find to answer a question. All my incentive is in earning an acceptance of my answer, rather than just in having an answer good enough to not not get spam-binned that sits there and feeds me pagerank.
I have seen reputable open source software developers put paid linkspam on their personal websites. When I called them out about it, they said "ha ha, I was wondering if anyone would notice that, yeah, they paid me a pretty good amount of money for that."
Trusted contributors could easily be bought off. Someone who was sick and tired of StackOverflow after putting way too much time into it, who was offered the right amount of money? Hey, you know, it might be worth it to make a few bucks instead of a few more meaningless internet points.
If you just make the threshold so high that only the very top contributors are nofollowed, then only that small cabal controls where SO's considerable linkjuice goes. If you broaden your criteria, there are more and more potential corruptible people; and it becomes easier to generate a little quick and easy reputation with a sockpuppet that you can spam with a few times before you're caught and move on to another sockpuppet.
