It is pretty easy to see how the $499 model is probably being sold at a loss if you know anything about business.
It's very hard to define "at a loss".
It's easy to look at fixed, per unit costs. The parts cost x, shipping costs y.
The other costs (R&D, marketing, advertising, air conditioning for Apple stores) are much, much harder. Some are directly connected with a given product - but need to be amortized over units sold over a time period.
If you use a short time period, it looks like "at a loss". For example, let's say that 400,000 Ipads have been sold. Let's take IFixit's numbers, round down a little, and assume $200 profit on the fixed costs.
400,000 * $200 = $80M profit. If R&D and marketing cost $200M - Apple's lost $120M, or $300 per Ipad.
If you sell a million over the first year, and higher end units raise the average profit to $300 = you are close to breaking even. Sell two million, and the bucks are rolling in.
Knowing something about business means knowing how to tweak the numbers to your advantage. Also, note that all of the R&D for the Ipad has already been paid for. This quarter, Apr-May-Jun, the R&D expense for the first generation will be zero.