All,
Some basic rules which apply to captains and passengers, whether of an airliner or a ship:
1. The captain is always The Captain, master after God.
2. If the captain is wrong, see rule 1.
This does not mean his decisions can be completely arbitrary. For instance, if the company he works for has a rule which says no ham operations, he is subject to termination if he overrides that. If the company permits ham operations, but he considers there are additional considerations which in his judgement make that unsafe, he has the authority to make that decision. There may be valid temporary reasons, such as maintenance issues which while not unsafe impose operational restrictions until corrected. He may well be required to forbid ham operation under those circumstance. He will need to report that, and he may need to justify his decision to his boss. A pattern of arbitrary decisions showing poor judgement may lead to termination, or even loss of his Master's license.
By all means inquire before or complain after the trip, but in no case does he need to justify his actions to you. See rule 1.
73s,
Alan WA4SCA
Retired American Airlines Captain