That's just it, they are
not paying the price. The "free market" goes out the window when the government decides that the continued existence of your company is important to "national security", and abdicates their regulatory responsibility because you're special. Were Airbus allowed to effectively self-certify their planes in the US? I rather suspect not.
I don't know how you can look at this whole situation and think "yup, free market working as planned. Everything fine and normal!"
Besides, the reason we have regulations is because there are limits to the free market if we want to live in a sane society. Markets only find optimal solutions if everybody has perfect information, but in reality nobody has perfect information. You're free to choose between brands of honey, but it's expected that the government will ensure that no honey contains plutonium because 1) a consumer can't easily tell if it does and 2) it's assumed that everyone would avoid radioactive honey if they knew about it. Similarly, airlines are free to choose between aircraft, but it's assumed that none of them want an aircraft that will spontaneously and uncontrollably dive into the ground; it's the government's job to ensure that nobody sells such a plane.