It’s simple: now that the iPhone 3G is subsidized, AT&T is treating it like every other phone they carry. Let me explain:
AT&T subsidizes the price of every phone it carries, by about $200. So that RAZR phone you got a few months ago for free was actually about $200. You’ve probably seen these un-subsidized prices if you’ve ever damaged a phone and had to purchase a new one at full price.
The idea is that AT&T will make up that $200 over the course of your two-year contract. So about $8.33 per month goes toward paying down that subsidy. When you get toward the end of two years, you’ll be eligible for an upgrade, which is essentially the ability to purchase a new phone at the subsidized price, as long as you commit to another two-year contract.
Maybe not the most ideal plan in the world, but it keeps the apparent cost of mobile phones low, and gets people in the door.
When the original iPhone came out, the arrangement was unique: AT&T wasn’t going to subsidize a cent of it in exchange for some flexibilities they allowed to Apple (such as at-home activation). Since there was no subsidy, AT&T lifted the “upgrade” policy for existing AT&T account holders, and allowed them to purchase the iPhone at the standard retail price everyone else paid.
But the iPhone 3G is indeed subsidized, and so the upgrade plan is back in effect. If you currently use a phone subsidized by AT&T, and you aren’t currently eligible for an upgrade (you aren’t nearing your contact’s two-year anniversary), you will need to pay the full, un-subsidized price for the iPhone 3G. In this case, that works out to either $199+200 or $299+200, hence the $399 and $499 prices.
If you already own an iPhone, AT&T doesn’t need to get back their lost subsidy, so you get to pay the standard $199/$299 price.
Hopefully, this clarifies things a bit.
UPDATE: The new iPhone 3GS coming out has a similar policy, except that there is no grace for 3G owners since the 3G, unlike the original iPhone, is subsidized.
If you’re not near the point where you’ve paid off your subsidy — and usually that means being more than 18 months into your plan — you’re not eligible for an upgrade at the subsidized price. You can purchase an early upgrade for $200, which is essentially paying for a significant part or all of that subsidy, or you can purchase a plan- and subsidy-free phone for a $400 premium.