I've recently been reading/watching some videos and writings by Robin Diangelo on systemic racism - here's a great starting point: https://www.youtube.com/watch?v=h7mzj0cVL0Q. She also wrote the book "White Fragility".
Thinking about that, I'm just wondering how different it would be if one of those people who mistook the employee for the CEO instead turned to the CEO and said "I'm sorry, please excuse me for the instance of racism I just perpetrated against you, I promise it won't happen again." I realize how outlandish that may sound writing that out, but I'd propose that the fact that it does sound outlandish is the main problem. Everyone in the US was raised in an environment that inculcated certain racial ideas, subconsciously or not. We can't address them if we're so embarrassed by their existence as to pretend they don't exist.
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.