Those came later (late '90s-early '00s), and ran mostly on Windows; believe it or not, at that time there were people that used Linux or Mac (I dual booted, Wintendo for games, everything else on Linux).
And most malware came from shady sites. Again, if you were careful, you rarely got it (rarely, not never). If you were not careful, well, it usually was obvious because even if your Windows was not infected with a virus or trojan, your browser would be full of toolbars and the PC would run like crap.