>> Anyway, the fact that pilot is in full command of the plane doesn't mean that he should be able to bring onboard whatever he desires, does it?

Do you take whatever you desire to work? No, because you don't want to lose your job because you brought in a playmate of the month calendar and a gun.

Its a job to them same as anyone else.

Aha, we should leave it to pilot to decide what he brings onboard. After all he doesn't want to lose his job, right?

We may also totally skip flight school certification requirement - after all pilots don't want to die either, right?

I'm really not surprised that you missed the context all together.