The Trump admin was very creative when it came to Harvard and figured out many different pressure points to push all at once. Don't expect it to be too simple. The guys running this have thought about avoiding the easy dismissal: https://www.ortecfinance.com/en/about-ortec-finance/news-and...
Just look at how the recent flag burning EO was worded in order to get around 1A concerns.
The Wikimedia Foundation does not depend on US government funding and even if the US somehow made life difficult for donors, they are sitting on a substantial endowment fund that can float them for a long time.
And at some point, if the harassment gets to be too much, Wikimedia can just up and leave. There's no reason that the Wikimedia Foundation needs to be headquartered in San Francisco, it could just as easily be in Oslo or Paris. That's a huge advantage that Harvard didn't have.
If Trump wants Wikipedia gone he'll just sue them or open an investigation that never needs to ever go before a judge. Then in return for dropping the suit/investigation all they need to do is make sure that a friend of MAGA sits on the board and can make sure that certain edits get approved and others don't.
People who are surprised by this or still assuming that he can't/won't do something because of the law or norms or "but then the Democrats will do X" need to wake the fuck up.
These people are going to do whatever the fuck they want under whatever justification they can cook up, and they don't fear any repercussions because they are not planning to turn over their new-found power to anyone else.