Edit: why do you think business lobby groups are constantly asking the govt to reduce VAT? Have you ever heard of the demand curve?
You're not selling the product for $100, you're selling it at $83.33 plus VAT. That means your customer will have to part with $100, though. If your customer is not willing to pay >= $108 for the product (i.e. $90 plus VAT), of course you're operating at a loss.
You could argue this is just semantics but B2C retail is the only major example where VAT matters. And considering we're talking about Apple I'm not convinced Apple's profit margins have Tim Cooke worried about EU VAT.
In the vast majority of cases, an enterprise software company will collect far more VAT than it pays out, so it's not zero sum.