You completely missed the point that was made.
When you persecute people and infringe upon them, it is necessary for their own good and their own existence to push back. Do you think gay people like spending so much of their life fighting for gay rights and equal treatment under the Constitution and the safety of not being beat to death on the street for simply being gay? Or do you think they would rather just have the equality and the safety of every other human being and carry on with the rest of their life?
Those "uppity gays" and "uppity negroes" and "militant atheists" that religious people usually say "should just shut the fuck up if they don't believe, because then it doesn't concern them" are "uppity" and "militant" precisely because they have to be active in fighting against the way they are treated, dismissed, and impacted by those who are intolerant.
Of course, not everyone can afford the time or personal/professional risk of being militant. Thankfully, there are those that make it their life-long cause to do that for the rest of them.
It is also hypocritical to call people "militant" who are just standing up for their rights and pushing back against your imposition upon society. I would say the "militant" ones are those who are using law and mob-rule to impose their religion upon politics, government, education, law, and all of society. Making comments about people being "animals" based on the tone of their skin or suggesting we should murder them so they "can meet their maker and find out how wrong they are about religion". THAT is militant.
It's a rather perverse and sick tactic to push and bully someone pretty much forever and then, when they stand up for themselves, shout "he's being intolerant of me!" (or, in some cases, trying to discredit lack of belief by claiming it is as much a religion as belief -- when it is the non-existence of belief and nothing more).
I imagine there were a lot of dudes, like yourself, back in the 1960s talking about how "all them negroes are actin' like nutjobs with all that marchin' and militant sitting in the front of the bus and drinking from white fountains and shit". (I am not trying to implicate you as a racist or anything, but am just drawing parallels between the attitude and terms exhibited by those in multiple situations to dismiss, diminish, and denigrate other segments of society who are actively demanding fair treatment).