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They don't charge anything for the content.

They do have an income source, though.

Their income source is donations. They do not monetize their users, so an increase in users is pure cost.

I'm talking about the "Earned Income" section they show here: https://khanacademyannualreport.org/financial-information/ (you have to scroll down to the second piechart)

It's separate from donations and gifts.

It's a non-profit educational organization.

It’s primarily a free website.

they are non-profit

Non profit does not mean zero income.