I remember hearing that the structure they have, where a for-profit company (Mozilla Co) is owned by a non-profit (Mozilla Foundation) is highly unusual, which of course is going to attract scrutiny.
Now there's all this Drumbeat Festival stuff, etc.. coming out the foundation. Clearly they are trying to position themselves as a non-profit that advocates for the open web rather than just a company that gives away a browser. Owning a corporation that gives away a browser is just part of that cause. Hopefully that's how the IRS sees it.
Sadly, I don't think a lot of the foundation sponsored stuff really ever links up with anything happening on the corporate side. At least from the outside, it still looks like the corporation wags the foundation and not the other way around.
Edit: Yes, the foundation does own the corporation.
I definitely agree that the corporation appears to wear the pants in the relationship, but there is still a lot of link up that is organized by the foundation, especially with the Mozilla developer network stuff.