"I thought that the tower was there to ensure the safety of the flights and the responsibility of that was on them, and not the pilots."
WRONG!
The phrase "pilot in command" means just what is says. Tower, or in-flight vectors for the pilot flying IFR are only advisory innnature.
The pilot always has the option of refusing ATC and either asking for alternatives (the usual course of action) or stating his intentions. FAA may be vilely vexed, and if his case for so doing isn't a good one, consequences occur.
But the pilot is not only always the first on the scene of the accident, he is always where the buck stops.
I don't understand why there is a problem with people accepting that the pilot makes the final decision.