I agree with you that "questioning why" it generally a good thing for understanding. The issue here is one of communication, whereby the connotations of "just" may be taken differently by Asker and Responder.
A Responder could take the use of "just" as implying "obvious thing you personally missed" which derides your efforts/understanding/intellect/ego.
Whereas I see the use of "just" as saying something about the Askers mental model. The Asker knows their mental model says this is easy. The Asker knows you did not do [easy thing]. They want to know why there is a disparity.
Anecdotally, I have been hobbying away when my wife walks in - is given a brief explanation of what I am doing - says "Why don't you just [xyz]?"
She has limited information. She knows it. I know it. We both know her mental model is not like mine. But through her building it how she wants we can explore options. When she says "just" it is because her mental model says this should be easy.
And sometimes I eat humble pie because it is. Because my mental model was built from scratch from a different direction and my perspective means I didn't see [easy thing]. Not often. But often enough that I appreciate every time my wife asks.
Maybe the issue is who/how often you are asked the "just" question. Are you being bothered by too many people who don't-really-know/don't-really-care ? Then the Nth person coming up saying "why don't you just?" is another time/attention sapping interaction.