You have to remember this was the 90's and it was a different time back then. I think there's a tendency to compare Windows in the 90s with how Linux is now. This was the same era as Mac OS 9 where a single application could still crash the entire system.
Exploiting common faults in Linux system software was pretty easy back then too.
From my perspective, Windows doesn't seem to be less secure but it has a greater share of users who do stupid things.