One of the biggest problems with Stack Overflow, and this applies to Reddit as well, is that it's not a viable business model. There's nothing monetizable about the "core business" of asking questions and getting answers. If there was, Quora or Experts Exchange would have prevailed instead.

Finding the right nonprofit structure to handle this need is difficult. And you could always end up like Wikipedia instead, which seems to spend 90% of its donations on things other than its operations, and yet cries that it will shut down if you don't donate your next latte (but I don't drink lattes...).