Hasn't stopped them from cancelling popular shows before. We call those shows "FYGRTM - f*** you, go read the manga." Sometimes it's because there's not enough material to keep going, other times it's because of a falling out between the manga artist and the anime studio (Kare Kano being the most famous example of that), but quite often it's because they don't think the show is making enough money.
They'll finish out the season, wrap up the story somehow, and call it done. If you are lucky, they'll resume the series in a few years when more material is out (Full Metal Panic!) and if you are very very lucky, they'll redo the series entirely (FMA Brotherhood.)
But most of the time, they stop at the end of the season, mid-story, and just never resume, because they won't recoup the production cost via advertising or toy sales.
In the case of Naruto, it's clearly still got enough of an audience to justify making more filler.
Some other examples: http://www.dramafeve...he-manga-ended/