"We can't create a culture that says it cares about diversity and then excludes almost half the country because they back a political candidate," Zuckerberg wrote. "There are many reasons a person might support Trump that do not involve racism, sexism, xenophobia, or accepting sexual assault."
Certainly there are reasons, but that's not the point and not why Project Include won't work with Y Combinator. Support of Trump involves considering sexual assault, racism, sexism and xenophobia to be acceptable. That holds regardless of the reasons you have for supporting him. Project Include is saying "No, those things that Trump loudly and proudly stands for are not acceptable, period. We don't care why you think they're acceptable because we don't believe there's any reason you could give us that could make them acceptable.". And this isn't just the candidate's supporters espousing those positions, it's the candidate himself making his enthusiastic support of those positions the centerpiece of his speeches and campaign.