A captain refused an off line pilot a jumpseat. There was no problem until the jumpseater came onto the airplane and introduced himself as an FFDO. At that point the captain decided he could not offer the jumpseat. Though he was smart enough not to say it was because the jumpseater was an ffdo it was apparent that there was not an issue with the jumpseat, until he found out that the jumpseater was an FFDO.
The jumpseater reported the incident to the ALPA jumpseat commitee and it worked its way around the system.
Both the captain's chief pilot and the FBI had meetings with said captain and explained to him that his authority ended where the FFDO federal badge began.
If and when you try it I am sure you too will get to have a meeting with a couple of FBI agents. They will explain it to you.
There are a few captains who make LEOs put their weapons in the cargo hold. Some have tried it with FBI agents. That did not work out too well for the pilots involved either.