The 3DS has become healthy and games are selling well, but Nintendo's still losing quite a bit of cash. The company recently increased its fiscal year-end expected losses from ¥20 billion to ¥65 billion.
From the beginning of the fiscal year up to December 31, Nintendo posted a loss of ¥48.35 billion, down from a ¥49.5 billion profit from last year. The strength of the yen has been partially blamed for the losses, although Nintendo has also said that the 3DS' slow start has had a significant effect.
Still, the 3DS has now shifted 15 million units worldwide, so maybe it'll start strong when the fiscal year begins again after March. Then we'll have to see what the Wii U does for the company (or to it).