Do anime usually lose money?
Anime is much bigger in Japan. There are lots of mangas that were given a shot at anime adaptation, but they didn't get a following and eventually got pulled. In my opinion, the manga has to be popular in Japan first before the network heads start to export the anime officially. 

There are other reasons aside from profit. Take Gintama for example; I can't be sure if they were pulled off air because of profit (which I doubt) or because the network wasn't happy with the show's direction.

So, yes, the big reason why they get pulled off air is because the anime didn't make enough profit. It's a competitive market.