Games Industry reports that Nintendo are selling each Wii U unit at a loss. This was confirmed by an unnamed Nintendo representative. The GamePad is likely a large part of why production is costly, but obviously the lacklustre sales also hinder some savings that come with larger scale production.
A lot of gamers where probably hoping that Nintendo would be lowering the price of the Wii U as Microsoft and Sony introduce their next-gen offerings this fall, but perhaps Nintendo will refrain from this as they've historically been a company very unwilling to sell hardware at a loss. Perhaps we should be expecting more aggressive bundles instead to give gamers increased value when opting for Wii U this holiday season.