Maybe the pilots aren't scared of armed marshalls, but they are simply using this stated priciple to avoid working.
Or, a more frightening scenario: What if they actually don't fear the armed marshalls, but it makes for a convenient excuse? What if the pilots themselves are so convinced that a terrorist plot is in the works that they themselves are too afraid to fly, DESPITE armed marshalls on board? Wouldn't that be a doozy? If an armed marshall has been assigned to a particular flight, there is plenty of cause to be concerned about that particular flight. Object to the armed marshall, don't fly, avoid what appears to be a higher risk flight!