It could mean motion but it could also mean just standing.
'Why are you standing up when you could be sitting down? '
That most likely means some is standing but there are seats available. No motion at all. Up and down are some kind of reflexives here I think.
You're right though it could mean you're actually in the motion of standing up.
I interpret VladaFu's comment as meaning that Czech has verbs that differentiate between the action of standing up and being in the position of "standing up." So, looking at the bright side, we got a learning bonus with the stealth introduction of the "motion" verb. :-)
Yeah, I picked up that introduction from this! Also realized how weird it is that we use these 'up's and 'down's with verbs when there's no motion and how frustrating that must be coming from a language that's so much more clear about it.
I took his comment to mean that he thought, "Why are you standing up?" should be incorrect because he believed it necessarily implies motion.
The basic meanings would be the same, but the version with "standing" is much more common
I'd say that "Why do you stand" is not much used as a simple question, but instead with some context around it: Why do you stand (with your broken leg) when you could sit? Why do you stand there (like a statue) when you can see I need your help lifting this really heavy box? That sort of thing.