"From an ultimate decision-making point of view, the Foundation is mainly just me. [...] It’s worth noting that the Foundation was created purely to be a trademark and IP holding entity that Automattic could transfer its ownership of the WordPress trademark to. There are no “members.”" [0]
[0] http://wpkrauts.com/2013/leaders-and-the-greater-good/#comme...
In addition, having counseled clients on this structure, the benefit of creating a nonprofit and giving it IP is that it creates a public check on anything to do with that IP. For example, while a startup's founders can sell the company, they can't unilaterally agree to sell off the IP in the nonprofit, and the public can challenge any such sales by recourse to a state attorney general's office.
It's not perfect, but it helps protect the IP in the way founders want to. In many ways, it's a one-way decision, which is why it works.
(Yes, IAAL.)