(This is a much better way of quoting, I think i'll do this in the future. Thanks :3)

The problem is that many people who are making reasonable points,
like someone who's pointing out that gems named "rape-me" really aren't
acceptable in polite society

That's not a "reasonable point", unless the question of "why does a program name equate to polite society?" is also being addressed at the same time. It's telling something people they already know (Hey! Did you know? These gem names are politically incorrect! This should make you upset because it will make some people feel uncomfortable!) - something which is usually not done unless there's some kind of ulterior motive.

It's politically correct, insensitive, and probably a lot of other things, I think pretty much everyone, including the guy who wrote the gem, could agree on that. Now what do you suggest we do about it, if anything?

Hemming and hawing and "How could they!"-ing not only accomplishes nothing in the great majority of cases, it turns people off of whatever valuable input you might have. Put another way, I don't think a way exists to say "This isn't PC" without coming off as a PC crusader.

There may be a few extremists out there, but not many.
What you see lots more are people who are tone deaf..

Ok wait a second here. With all due respect, that is completely and utterly your opinion and not any kind of objective fact. All I said were that loud extremists exist (something you appear to agree with me on), and implied that they are unpleasant to deal with and cause more problems than they solve.

A safe space is instead one where you feel comfortable telling someone
when you think they crossed the line, that they will respect that and
not attack you for it.

That's not how I've seen the term used, unless you expand out "respect that" you mean "police their speech and avoid offending anyone".

Think to yourself. If you have to tell someone "this is not a safe space",
you are basically telling them "I do not want you in this space."
Because if you want them in that space, you will make it safe for them.

Only if you accept the social justice definition of "safe", meaning "you absolutely will not have your feelings hurt here, and we'll smack anyone that does so.". What if the feelings of other people are not of primary (or secondary, or...) concern of your particular group? What if I do want someone in this space, but I expect them to be able to brush off some amount of non-PC dialogue because it's quite frankly not all that important to the group's goals? Is that expectation wrong? (Or worse, evil?)

On the public internet, recall that you can never be sure of who will
see your joke, and how they'll react to your humor. Things you post
to the public internet should be things that you are OK with your
wife seeing, your grandparents seeing...

Your vision of the public internet sounds incredibly dry and boring to me. Where does a place like 4chan fit into your world? What about a Carlin standup routine? South Park? I like the idea that I can go on a social network site and talk smack with friends the same way I do in real life. I like the idea that places exist where people can talk about whatever they damn well please, and if anyone else doesn't like it, they are free not to listen, regardless of their meatspace background.

Indeed, that seems like the only idea that scales.

I'm curious why you call out minority rights groups.

You misread. I wasn't "calling out" anyone, I was saying that it's socially unacceptable to call out a minority rights group for behaving badly if and when they do, because then you are seen as the enemy of whatever that group is campaigning for. The hive mind effect there is quite strong.