I feel like this is a slippery slope. As with all neutrality, net neutrality means that for good or bad you can't prefer some traffic. Any zero-rated service is not neutral. You can't block Facebook from being zero rated but allow Wikipedia.
You can give tax exemptions to Wikipedia but not Facebook. Why then not also zero rate Wikipedia but not Facebook?
At an operational level they're not much different; both rely on generation of revenue to cover costs and to compensate their permanent staff, and both can make profits which can be reinvested in the organisation or distributed as dividends or spent on 'stuff'.
Essentially the only operational difference is that all of the non-profit's untaxed profits must originate from activities aligned with their primary stated function, whereas Facebook is free to earn from other unrelated business activities.
Furthermore the officers of a non-profit can't dip into the profits for self-enrichment since the profits belong to the organisation ( hence untaxed ), but since they extract their remuneration upstream of the profits that's not a major issue.
What made it even more iffy was that it would've been free on select few services and they planned to include a couple other companies later, it took a lot of convincing and explaining by a lot of concerned people. It was a scary time and no one wants to go through all of that again for whatever reason.
i'd rather wikipedia was subsidized, because otherwise the people who benefit the most from it have relatively more expensive access to it than the rest.