I'm guessing the authors deployed to production with no indexes on their collections. This means the cost of most queries was probably O(n). This could go unnoticed in development where N is small, but is unacceptable once you have any real data. I think they are recommending thinking about and adding indexes while you are developing as opposed to trying to do so post-hoc, once queries are taking tens of seconds.

MongoDB is basically unusable without indexes even under the slightest load.