Dragons needed to be hidden from human view over 1500 years ago because there was a huge problem related to these creatures in the past and their extinction was almost inevitable. The problem was that many hunters would do anything in their power to capture a dragon because the flammable liquid they carry inside them was extremely useful as an antiseptic that basically healed people from all kinds of ailments with ease.
The dragon teeth and their skin was also useful for many different medical purposes but the teeth seemed to be south after by the higher classes for jewelry and this is why they sold for a fortune. This is the reason why the order decided to hide them and they are being kept in a location underground that is basically like a huge bird cage for dragons. They can fly freely and we have seen the birth of hundreds of them in captivity.