Most of my other opinions have already been expressed in posts above, but I would like to add a few thoughts (in no particular order):
In my opinion, non-profits are like for-profits in that some are good, some are bad, most are probably somewhere inbetween. All are run by human beings, and therefore rife with opportunities for misuse, innefficiency, and hypocrisy, as well as opportunities to be well-run, well-intentioned, and beneficial. As with people, I'm inclined to take them one at a time.
I think re-naming non-profits is unlikely, but I wonder if there are other ways to improve this?
Is this an opportunity for a Wheaton Labs experiment? A better way to run a non-profit?
In the monthly-ish email that led me to this thread, Paul details that permies.com runs in the red and that many projects and events at Wheaton Labs are unprofitable and largely funded by Kickstarters. My question here is, is this unsatisfactory? If so, since permies.com and Wheaton labs are all about experimentation, MacGyvery, and out-of-the-box thinking, I hope Paul and co. are actively working on new ideas to improve or fix this.
I have a relative who has worked for non-profits and looked into starting her own. The main problem for me is that a non-profit is required to have a board of directors (this may vary by state). So, no matter how much I trust the people I choose to be my board, technically they are in charge, and technically they could fire me! I'm enough of a control freak I don't think I could live with that, so I'm not crazy about the non-profit route, and I don't blame Paul for not taking it.
I think venting is sometimes valuable, but I also believe that unless you're thinking towards improvements or solutions, it can quickly end up just being angry at bad guys. And in that case, like Paul, I'd rather just move on and try to make the world better in my own back yard.