Well, it appears there are two different organizations, the Mozilla Foundation--which is the non-profit--and the Mozilla Corporation--wholly owned by the Foundation, it is a private company.
On the page you've described: "For each individual whose compensation must be reported in Schedule J, report compensation from the organization in row (i) and from related organizations, described in the instructions, on row (ii)."
For Mitchell Baker, Brendan Eich, and James Cook, they all have their salaries and bonuses listed on row (ii), indicating it's from a "related organization". Further down a few pages, the only related organization that is listed is the Mozilla Corporation.
Ryan Merkley, Mark Surman, Christopher McAvoy, and Christopher Lawrence are the only people who are listed as having their salaries paid by the Mozilla Foundation, and their salaries are much more modest, in the range you had discussed.
I don't know how Mozilla Corporation makes its money.
EDIT: this old page says "contracts with Google" http://www.technobuffalo.com/2010/01/01/how-does-the-mozilla.... I suspect those have been replaced by "contracts with Microsoft" now that Bing is the default search engine. It would suggest the CEO is not in any way being paid with donated money.