Indeed. If the BoM is even half-way right they were paying roughly $300 and $350 for 16GB and 32GB units respectively. At $400 they would be making a gross profit, but after R&D, support, and advertising, it's hard to imagine they were still turning a net profit.
Also keep in mind they have to give room for the retailer to mark it up. So if MSRP is $400 for a tablet, Best Buy might only be paying something like $350 for it. Then factor in defective units, returns, etc.
The iPad is unique in that there is almost no discount when they sell it to the retailer (reportedly 3%). Retailers don't mind not making money on the iPad itself because they sell very easily and they can make up for it by selling accessories and extended warranties. Best Buy currently dedicates a LOT of floor space to tablets that aren't selling. You can bet they'll be reevaluating this in the future.