Well, it's a selling point, no matter how you slice it. And with over 15mil sales in its first year, I'd say its not a bad one!
Nintendo may be losing money on it, and yes, it's likely because of the cost of the 3D screen. But in a few months, they'll be making money off it again, and, as such, will likely dominate the market and be back in profit very soon.
The 3D is a nice feature. I enjoy watching cutscenes with it, even. But I don't use it all the time. Doesn't mean it's a bad idea.