“Well, firstly, I think the charges of militancy and fundamentalism of course come from our opponents, the theists. My rejoinder is to say when the boot was on their foot they burned us at the stake. All we’re doing is speaking very frankly and bluntly and they don’t like it.”
While you can say this is merely because civilisation has progressed, “believe in what I say or we’ll kill you” has a different ring to it than “we think you’re being a little foolish and causing harm in the process”. This view also begs the question of why civilisation has progressed.