Why should it matter if MMM is making money or not? It's not a public service he's doing here, after all, it's just a hobby that happens to be popular and grow a community of followers. Monetization of something doesn't flip the corruption switch, and likewise, it's still up to individual readers to click ads, sign up for credit cards, or follow reference links. I could have typed Betterment.com into my browser, but I chose to click through MMM's links - because I like MMM and I want him to continue his good work here.
And, as far as "Where is the money going?" Well, I would imagine it goes into a lot of investment accounts :). But really, that's nobody's business.