I get what you're saying. Asking somebody where they're from is trivial and there's no rational reason for a person to get worked up over it. But the issue with micro-aggressions, as I see it, is that while each individual action is trivial and insignificant by itself, their cumulative effect over many such actions is to create an unwelcoming and hostile environment.
To continue the hypothetical I made up earlier, consider a third-gen college student of Vietnamese ancestry. This person was born in the US, doesn't know a lick of Vietnamese or Mandarin or whatever, plays Fortnight in his spare time, listens to whatever groups are popular in The Year of Our Lord 2019, etc. In other words, he's as American as you or me. He goes to college someplace rural and white, where he stands out as "foreign looking."
On a daily or near-daily basis, somebody asks him where he's from, as if he's not American. He has to explain whether he's
Chinese or Japanese. He's called upon to be the Official Spokesperson of Asian People whenever an Asia-adjacent topic comes up. Everybody assumes that he's good at math, and people do a double-take if he's studying something non-STEM-related. Locals speak more slowly to him when they first meet him because they assume that English isn't his native language. Nobody mentions sports when making small talk because of course nobody from Vietnam would know anything about the NFL. And so on.
Each of these individual things, happening once in isolation, is no big deal. None of them are examples of overt racism or xenophobia or ethnic hatred. Some are even well-intentioned. But they have the cumulative effect of forcing this student to spend mental energy shrugging off a stream of small offenses, which is something you and I never have to contend with as white guys.
Now sure, at some point this student is going to have to figure out a way to just deal with this sort of stuff. But I can do my part in trying to put myself in his shoes and avoid doing the sorts of things I mentioned above. It's just an issue of mindfulness.