Usually by tracking web activity. Your computer informs every web site you visit what type of operating system you are using, which web browser, etc. Of course, you have to statistically adjust for how likely someone is to defeat that; Fewer than 1% of Windows users do, but upwards of 30% of Linux users do. Are those numbers solid? No. But if Linux numbers should be adjusted up to 1.2%, instead of 0.9%, does that change the truthfulness of what I wrote?
Otherwise, you could compare a Linux download to a Windows sale. My guess is that greatly overestimates the portion of users using Linux, since a lot of people use it for limited purposes. (I’ve downloaded various Linux flavors a good dozen times, but bought a Windows-loaded computer only about four times.) But that’s still a whopping 2%.
I have not seen Linux at only 1% or anywhere near in the last ten years, even on Windows-centric sites it runs at least 3-4%.
You may be seeing something else, but I'm not seeing Linux as insignificant, and I'm seeing Mac as much higher than you claim as well. Likewise, the trend I'm seeing over the past year is Linux is growing at the expense of Mac, mostly, but Windows is declining a bit as well (about 3% over the past year, about 4% over the past 2.)
XP is still the most popular version, at 63%, of all Windows hits over the past year. Vista is number 2, at 25%, and 7 is just getting started at 3.5%. I see as many hits from NT over the past year as 7. But the trend is that Vista and XP hits are declining in favor of 7, with XP dropping to about 59% and Vista to 18% with 7 picking up the difference.
Anyway, that's what I'm seeing these days. I don't see Linux at all as marginal as you're seeing it. *shrug*