First, so we are on the same page: An LLC and "a non profit" are two orthogonal things. "Non-profit" is a tax status granted to any entity recognized by the IRS, an LLC is a state construct, not recognized by the IRS.
LLCs exist in the court system - they can be liable for things done under the legal umbrella of the LLC, meaning they be sued, and so on. This is the "Limited Liability" part; the members of an LLC are, for some things, not personally liable for any legal trouble. LLCs do not exist, as far as the IRS is concerned.
Because of this, an organization can be an LLC in it's local state, registered as a corporation of some kind with the federal gov't - and that corporation can be Non-Profit; eg; an LLC can be Non-Profit, and nothing can be "a" Non-Profit, because Non-Profit is not an entity, it's a tax status.
So.
You are Mark Zuckerberg. You hold a lot of Facebook stock, and you want to commit that stock to Philantropy. Cool. You could start a federal corporation (which would be recognized by the IRS) and file for Non Profit status.
But why would you? You're not accepting other peoples donations, so you don't need to help them make tax-deductible donations. Your money, "moved into" the LLC, still goes on your personal taxes (remember, the IRS does not care that your state has invented some court construct called an LLC - unless you're a federal corporation, your money goes on your regular tax return), meaning any donations made to, say, a Non-profit research fund, will be tax deductible just like it would any other day, so you don't loose out on any taxes.
Creating a Non-Profit of some kind would mean a lot of legal work, a lot of complexity in terms of how this new federal entity uses it's $3B Facebook stock to vote, if you set up as a foundation there are rules around holding too much stock in individual companies, et cetera et cetera. TL;DR: There's a lot of downside and the only upside is that some guy on Reddit would whine about how you're a fraud in some other way.
If I wanted to set aside $3B of my personal stock and tell the world "I'm gonna donate this money, over time", I don't see why I wouldn't just pay the $50 filing fee to get some legal distance from lawsuits in the form of an LLC and call it a day.
Edit: I should say that this is a short-term perspective. I would expect, as Mark grows older, he may want to move this money into an actual non-profit entity of some kind, with a board and so on that could oversee the management and dispersement of the money over the long haul, or whatever. But in the short term, it just seems like a lot of legalese for no benefit.