Hypothes.is has kept to their belief in being a nonprofit organization by collecting all of their funding from donors and their major kickstarter. In their "FAQ" section, they explain that they resist corporate sponsorship due to the fact that "it is difficult to preserve journalistic objectivity over a long time period as a commercial enterprise". They believe that being under a corporate sponsorship puts pressure on them to make a profit, which is not their original founding message. By being able to independently generate funding, they can focus on what's ahead of them instead of how to monetize their product.
They have three main foundation backers: The Andrew W. Mellon Foundation, The Shuttleworth Foundation, and the Alfred P. Sloan Foundation. There are also many users who have donated money to Hypothes.is through their kickstarter, which raised about $230,000 from individual donations back in 2011. They're also regularly taking donations through the main Hypothes.is home page.
I feel like being able to take donations and money from users and contributers really allows Hypothes.is to take full creative control over their product. Since there is no larger structure they must answer to, they can truly focuson their mission statement and maintain their own journalistic integrity.