As it should. The 3DS is a handheld. Handhelds and consoles sell to two different demographs. One is mostly for children, the other is for both childrend and adults. One is ultra cheap, the other is expensive. One is portable, the other is not.
When handhelds are outsold by consoles, something is terribly wrong. It would be like Lexus outselling Toyota.
Lexus is owned by Toyota. But yea that would be weird lol.
A home console does not usually outsell handhelds until big releases, that is for sure.