The Bill of Rights (the first 10 Amendments to the Constitution) limit the government. The Articles of the Constitution assign the rights and responsibilities of the government.
> The govt has no right to prevent us from flying
You have also misunderstood the Constitution. The government does have the right to limit our individual rights either because we have lost them after due process (eg. you have no right to fly if you are serving a prison sentence) or due to national security actions (eg. you have no right to fly if the country grounds all flights like it did immediately after 9/11).
Inalienable rights cannot be taken away by governments, which don't have rights. That there are temporary exceptions for prisons and emergencies is inconsequential to this thread.
> The govt has no right to prevent us from flying
You have also misunderstood the Constitution. The government does have the right to limit our individual rights either because we have lost them after due process (eg. you have no right to fly if you are serving a prison sentence) or due to national security actions (eg. you have no right to fly if the country grounds all flights like it did immediately after 9/11).