Few people ran linux on the desktop back then, even most developers ran windows.

Everyone just installed bitcoin and ran it once then forgot about it, so starting it at login and running it in the background was the simplest way to increase the number of nodes online at any given time.

A Linux build wouldn't have really helped much in comparison; no one was going to run a server just to try it out (and there weren't easily deployable VPS's etc like today).