Businesses are made of people. But your argument is even less coherent than that. When people boycotted Nestle, they were supporting a campaign whose intended impact could have put thousands of people out of work, many of whom had no opposition at all to the boycotter's ideas. Boycotting a company is an even more grave act than criticizing some dude with more than one McLaren about endorsing a Trump campaign surrogate who could most likely buy McLaren Automotive. But we tolerate and accept boycotts, as we must, because they are a form of political speech.
It is totally fine to take action against a business; that the business is comprised of people who have no direct input into the actions of the entity and may face consequences of the actions against it should not be an important consideration of where you choose to spend your money.
A counterexample would be a situation where someone went and figured out that most of Nestle's employees were supporting Trump and then boycotted the business as a way to pressure those employees into altering their positions. That is much closer to being morally objectionable.
Outside of that, Altman _has_ criticized Thiel's views, directly. The disagreement seems to be about what to do afterwards. He is simply not willing to cut him off for this disagreement. If this way of thinking was a social norm, you would eliminate "anti-PC" griping which is important to a good chunk of Trump supporters, and you would likely see positive social change happen more rapidly (e.g. if this was the norm 50 years ago you might have seen more movement on gay marriage, etc. if people could pipe up without fear of being fired (or "boycotted")).
