I worked at a computer shop at the time. Few consumers wanted the Linux versions: they all chose Windows. I'm not sure the license was free, as the Windows machines were more expensive with the same hardware.
So I checked on the Internet Archive; we sold the EEEPC 900 with Linux for €329, and the Windows EEEPC 901 for €409. The Linux had a Celeron M and the Windows an Atom N270, so I guess I misremember them having identical specs.
I assume the Atom is faster(?) The XP machine felt slower though.
Either way: people wanted what they knew, which was Windows, and they paid more for it. I wrote about this before: https://news.ycombinator.com/item?id=41431733