Many people have areas of ignorance or incomprehension, or nonstandard opinions, about which they feel a bit insecure: they worry that if they ask questions about these things then the questions will be seen as stupid, and by extension they will themselves be seen as stupid too. The "Stupid Questions" threads are intended to be places where these people can ask those questions, with the implied promise that no one is going to look down on them for doing so.

So:

• If you have a question that you are confident is not stupid and doesn't reflect badly on you for asking it: go ahead and raise it somewhere else (e.g., in the open thread).
• If you have a question that you do think might be stupid, or that you worry people might think you stupid for asking, you can ask it here and we all promise not to do so. (And you may also notice that lots of perfectly reasonable people are asking questions of broadly similar stupidity, and aren't getting attacked for it.)

I don't see what harm this thread does in either case. Unless you're concerned about the following scenario: you ask what you think is a reasonable question somewhere else, and the response is "Bah, that's a stupid question. Go ask it in the Stupid Questions thread." That would suck. Empirically, I don't think it's ever happened yet; if it ever does, I expect the rude person who does that to get heavily jumped on by more reasonable people.

An alternative might be some sort of global undertaking that any question, however stupid, is welcome anywhere and won't get jumped on. But I don't think LW should have such an undertaking. If someone asks, say, "why doesn't evolution contradict the second law of thermodynamics?" then I think they should get a very different answer if (1) they genuinely don't understand, know they don't understand, and are willing to be enlightened, than if (2) they think they've found a fatal flaw in a major scientific theory and asking the question is going to leave us all asking in abject humiliation how we can convert to their religion. In case 1 we explain politely and respectfully and, hopefully, everyone goes away happy and better informed. In case 2 a more critical tone is called for, lest third parties think the question is less silly than it really is.

Maybe you should work on that aversion ;)