If you're a VC coming to a first meeting with a startup CEO and their team, none of whom you have met in person before, making an inference at all is simply unprofessional. You should be asking. The fact that the VC's inference was that the white person must be the CEO just adds the further insult of racist stereotyping to the insult of unprofessional behavior in this context.
My main takeaway from the article was not "lots of people in the startup world are racist" but "lots of people in the startup world are unprofessional assholes". I think the latter problem is what needs to be fixed.