Nintendo has always sold their hardware for profit. They made money on the Wii from day one.
They're taking a bath right now because the strength of the Yen versus USD removes a lot of their export profit. That, combined with the fact that they're ramping up production of the 3DS and the next console, is the reason they lost money.
Nintendo's taking a bath for multiple reasons but in regards to the wii (1) they rode it for too long and (2) all it did was games while the more robust hardware in the PS3 and Xbox made them more useful.
That is why Nintendo is taking such a bath this generation. People buy a Wii for the novelty and only get one or two games where Microsoft and Sony are much more about the games they have on their consoles.