For instance, I'm no huge fan of Islam (or any religion), however, my beef is with the doctrine and the leaders, not the average day to day Muslim, so I'll actively speak out against Islamophobia and try not to offend the average Muslim. It's called actively not being a jerk.
The society we've built is by no means adult or responsible. Millions starve, get killed in genocides. Slavery is still rampant. Atrocities happen all across the world. Animals are treated inhumanely. The 1st world doesn't make much of an effort at addressing these problems. Why? Because people rather not talk about it or know the details about the truly horrendous things going on in this world. Ignorance really is bliss.
This status quo is only possible because we, responsible adults, choose to stick our collective heads in the sand. We need to get confronted with many things we disagree with and we have to stop passively supporting the status quo (unless we really think this is the best we can do as a species). In the big scheme of things hurt feelings don't matter.
If a vegan tells me with a smirk "If you knew where that steak came from you wouldn't be eating it" it's easy for me to get upset at the vegan for being a jerk, for ruining my appetite. But I wouldn't get offended if the vegan were simply wrong. I get upset because I know, deep down, that I would never set foot in a beef processing plant. Sure, the vegan is a jerk, but is he wrong?
Going with your example; substitute characters if necessary: You may not have a beef with the average day to day Muslim, but you do have a beef with people who have a beef with the average day to day Muslim. Even though your adult tolerance may just be based the comforting belief that the average Muslim is not the problem and that a few religious leaders are. The jerk probably believes that the average day to day Muslim is part of the problem. Who is right? That's a factual question about the world. And if it turns out, for whatever reason, that the jerk is right and you are wrong would you then change your mind? Would being a jerk then be justified? Or would you still choose the non-confrontational route and avoid giving offense? Is your true objection that only the Muslims leaders are the problem or is it a mere rationalization for politeness and civility?
(Questions are rhetorical. I'm not defending the sexism in the FOSS world, nor do I judge you for being tolerant.)