Because the purchase price isn't the unsubsidized price. Would you be ok if you walked into a car dealership, talked them down to $100 above invoice, and then had them charge you sales tax on the full MSRP of the car?
Or if you walked into a store and had them charge you sales tax on the full MSRP of any item, even though you're paying a sale price?
No, you wouldn't. It's just not done.
Sales tax in the US is a percentage of the purchase price at the point of purchase. For the subsidized 3GS iPhones, the purchase price is $199 or $299, NOT $499 or $599.