It's true there wasn't much going on for Nintendo most of last year. The 3DS didn't have the big games falling in till the end of the year and there were only a handful of games on Wii and DS worth noting that dropped in 2011. However, although sales were down, Nintendo switched strategy. They opened up about what the future holds, they started working to help 3rd parties more, the 3DS eShop started greatly advertising what's hot and what's new, big titles got pushed out the door, and sales went through the roof.
Seriously though, because they switched the way they did business, 3DS week by week selling more then any other system globally. Sure they're losing money on 3DS sales, but the eShop is now turning a pretty good profit, giving both Nintendo and developers a good income. Not to mention the eShop is advertising games which in term also helps retail software sales. Plain and simple, selling the hardware at a profit is NOT a problem, just ask Microsoft and Sony.