True. But those are fixed costs that can be spread out over millions of devices. Some estimate that 2 million iPad Mini's were sold this weekend (http://www.computerworld.com/s/article/9233257/iPad_Mini_iPa...). Given that a couple more millions will be sold in the future, you could accommodate $10mil+ for a few bucks.
Note that the 3 million figure is for both the new iPad and the iPad Mini.
ntm shipping
Shipping is inconsequential. How many iPad mini's fit in a shipping container?
A shipping container last time I looked cost $6k. Air freights really won't add that much cost to something the weight of the iPad, less than a dollar.