Paying for it gives you breathing space in the short term while you sort out your yields, keeps your marketing rolling, leaves your partners with something to sell. At some point it becomes better to sell anything, even at no profit, than to cede the market to your competitors and watch your partners and the market move over to the opposition. Nvidia is spending money in the short term to try and make money down the line.
The thing is, though, there's almost no lock-in for GPU's, and game developers don't pay license money to IHV's. Let's take a scenario, for example, where we have the following situation:
1. nVidia has a chip, but low yields. Can sell chips at some loss.
2. Three months later, ATI releases a product that is better in every way (price, performance, power, features, etc.).
3. Three months after that, yields on nVidia's original chip are finally to the point that they could have sold it at a profit against ATI's part, but now they have to lower their price and continue making a loss for a while longer.
Or, this situation:
1. nVidia has a chip, but low yields. Can sell chips at some loss.
2. ATI has no new parts.
3. Six months later, yields on nVidia's original chips are finally to the point that they can sell it at a profit. But now they have to make up for six months of losses.
In other words, selling chips at a loss in the current GPU market is basically lose-lose situation. You can make the money back if you're selling a closed platform, like Sony did with the PS3, because there they earn most of their money on game sales (some portion of console game sales goes to the console maker). There's also a good amount of "lock-in" for the next generation because only PS3's are backwards-compatible with PS2's, X-Box 360's with the original X-Box, and so on. By contrast, ATI and nVidia hardware are, to a large degree, just as compatible with respect to one another.