Because that's the deal they made with you when they started using it. "You may use this software free of charge for non-commercial uses. Commercial use is allowed under our [Commercial Use Agreement][0]", etc. etc.

You're selling software to companies with legal departments for an amount that, frankly, isn't worth the hassle of trying to scam you out of at the risk of you suing them. Companies really do pay for software based only on the software company asking them to do so.