The New York Times ad was paid for through donations to present an alternative to the closed ecosystem dominated by one browser that didn't follow open standards.
https://blog.mozilla.org/blog/2017/11/14/fast-for-good-launc...
Early versions of Firefox featured links to various news organizations and stories pulled from their feeds, until certain jurisdictions threatened to block the browser entirely.
At some point their missions may have diverged, but the marketing of both were closely intertwined. MoFo accepted donations and other sources of funds which it used, in part, to fund development of a browser by MoCo. Other projects came later, but the community's understanding of their respective roles remained the same.
As a long-term observer I followed this closely when the Foundation and Commercial split was announced, and remember reassurance s about the core mission being loudly proclaimed.
Here it is from the former CLW herself:
https://blog.mozilla.org/blog/2007/08/09/firefox-is-a-public...