I first used ninja taxis with my Mongolian friends, so I had a pretty friendly introduction because they were able to help translate and navigate everything. Even though a ninja taxi is a common way to travel, just like anything else, it's important to be safe when using it. I usually only take ninja taxis during the day, and I try to go with friends, especially at night. If I want to use one, I know that I need to be able to tell the driver the address of where I want to go (as they may not know where to go) and know how much is a reasonable amount of money to pay for a ride.
I think that part of the reason why ninja taxis are so popular is that Mongolia, in many ways, still has a small town feel to it. People want to help other people, and even if they make a little money on the side as they do it, ninja taxi-ing is a way to help provide their neighbors with public services that aren't always provided. In the future, ninja taxis might fall out of use, but for now, they are a great way to provide Mongolians (and me) with a convenient way to travel in urban and rural areas.