Salaries are a common thing that nonprofits spend their money on. That table shows some very comfortable salaries, but not at all out of keeping with an organization that size. There are many larger nonprofits with much larger salaries: a number of health care systems are incorporated as nonprofits, and their executives get well into the tens of millions.
You also get organizations like MITRE, a billion-dollar federal contractor that pays million-dollar salaries to its C suite. I'm honestly not sure how that's legal. The health care firms are dubious enough.
Still... the idea is that they're not trying to earn a profit for shareholders. They don't pay taxes on their profits because nobody owns that money. The employees who earn 7 and 8 figure salaries, they do pay ordinary income tax on that money, as anybody else does.
I really don't know how much actual work Wikimedia does and whether it's spending that $88M well or badly. But I can say that it is in keeping with the American tax system's use of the term "nonprofit", which is not really what people expect it to be from the word alone.
It was never the government's intent to determine which nonprofits are truly noble and just. It's also not their job to govern how well they spend their resources, or how big they are allowed to be.
If they are lying or defrauding donors, there are existing legal remedies.
So they limit tax-deductible corporations to certain categories that have some kind of benefit. They don't police it very closely, but if you come to their attention, they'll force you to pay taxes and possibly penalties.
[0] Including administrators. It's customary to say "btw I have never been paid to edit", completely unprompted, when accepting a nomination for adminship.
Look up the awardees of those grants; it is clear that they largely go to organizations supporting specific political narratives.
Honestly, the information being so easily available and transparent is pretty neat. Kudos.
When you donate to those nag screens you're funding something very different than servers to run Wikipedia, and they're not super open about that.
The Wikimedia Foundation manager takes $400k as salary.
