I donate to Wikipedia every year because I use the product almost every day, and I consider it paying for a good product, not a donation. They happen to be set up as a foundation where I can look at their financials, but in my mind I treat them more like a private company. If they want to waste my money then so be it. I pay what I think is a fair price for the amount of value I get from the product.
I think the crux of the argument is that the money is largely not going to improving the product, which is mostly done by volunteer editors and contributors, but it is going to a management class fighting over project funding for new initiatives. This argument may be out of date since they have had a huge management shakeup since it was written, but the criticism that volunteer labour produces the bulk of the value i…
When you decide to donate to a non-profit as if you were paying for a product, that assumption doesn't necessarily hold. In this case, you know fairly clearly it doesn't hold: the money doesn't go towards either the future development of the product, the continued existence of the service, or the motivation of people in the future to set up things like Wikipedia (no future Jimmy-Wales-in-2001 is going to be influenced by the 2015 Wikimedia financials). As a charitable donor, you cannot create such a nexus just by wanting it to exist.
(However, what you can create is a nexus between your charitable donation and the fundraising department of whoever you're giving to - all the more if you appear to donate in response to fundraising campaigns and not in response to the actual work the organization is doing.)
This is also why I'm a skeptic of large companies/conglomerates, which have the revenue to continue their existence basically regardless of any individual product. Very few companies operate internally on a market-based economy; they operate on the human judgment of whether management likes you and what you do. That means that a small new project that makes significant profit as a percentage of its expenses might still be a drop in the bucket of the company as a whole, and a politically-important project that's losing money might still continue to be funded if the company can afford its losses. The company might (entirely rationally) decide that "strategically" it should continue to invest in that product, which is to say that it should take advantage of the fact that it's not subject to the usual market pressures to drive out smaller or even differently-shaped competitors that are.