Unfortunately in my experience it is often followed by an explanation of why what I'm trying to do isn't what I should want to do, as though I am not aware of my own goals and constraints.
Sure, some people are assholes, but that's just people. Nobody's in your mind, they can't guess your requirements, thought process and level of experience. In my experience, more often than not, asking the question "why would you want to do that?" gets you a bad reason. "I did X this way because Y. I need Z." would filter the legitimate questioning out. From there, the others are just assholes, and those are everywhere.
As for the small differences in semantics, I'm not a native speaker, neither have outright negative connotations to me, but I feel like getting tripped up on such a small thing - and simultaneously assuming the interlocutor's intentions - is kind of overblown.
"Do", in the present tense, does not carry those connotations. It implies "I have acknowledged that your want is present and real, but I need more information about your context to be able to help."
Sure, but if I told a plumber they'd understand and help me find a solution to my problem. That isn't what happens on StackOverflow, instead they try to convince you that you have to change your problem to fit the solutions they're familiar with.