Another native speaker here: I think the fact that we can debate this is evidence enough that it's confusing :) Yes with salary I usually say I "make" my pre-tax income. But I don't know if that's really what "make" means per se, or if that's just a side effect of how most jobs advertise salaries in pre-tax terms. (Also I assume this usage is actually older than the income tax.) In my mind, if someone tells me they "make $X / month" from a business, it sounds to me like they're trying to draw a comparison with "making a salary of $X / year", which is a lot closer to profit than revenue.
I guess in the end, it's just uncommon to say something like "Microsoft made $X billion last year" by itself, because it's just not clear what it means. Business news articles will almost always phrase something like that as "made $X billion in profits" etc.
