In a cooperative that's true, but in a capitalist corporation, the equity is owned by whoever owns it, who can dispose of it as they see fit (barring any shareholder agreements preventing certain sales). It's not like Zuckerberg is going to give his Facebook IPO capital gains to his employees, or reinvest them in the business; he's going to put them in his personal bank/brokerage account. If he had donated 1% of the equity to a charity 5 years ago, the only thing that would be different is that his personal account would have 1% less of Facebook stock in it. None of the employees or the other shareholders would be affected.

When it comes to companies spending on things that their employees might find morally repulsive, I think political contributions are a much bigger problem than charity donations. Especially since those actually come from the company's revenues, rather than being taken out of an owner's equity--- I would have much less problem with political contributions if they were donations of stock by the company's owner, rather than checks written out of the corporate budget.

In any case, the most likely thing that 1% would go into if it weren't donated, in the case of startup success, is just luxury goods/travel for the founders. Do you really think a private jet for the founder is morally superior to donating to charity? What if some of the employees are morally opposed to private jets (e.g. on environmentalist grounds)?