No one implemented standards back then, and IE WAS the de-facto "standard" as it had something like ~98% market share. I'm not saying standards should have been made bug-compatible with IE or even that they should have gone out of their way to accommodate IE, but stuff like the box model which was 1) actually better (or, at the least, equivalent), and 2) a huge pain for everyone could have just been in a "CSS 2.2".
It would have reduced headaches for everyone, especially non-IE users as the people who suffered the most from this weren't the IE users and devs who only cared about IE, they were the Phoenix/Firebird/Firefox and Opera people and devs who cared about them. One has to wonder if uptake of things like Firefox or Opera wouldn't have been much faster in an alternative universe where these changes were made.
Mindlessly following standards just makes no sense. Also see GNU and POSIX_ME_HARDER/POSIXLY_CORRECT.
Apart from that, IE6 also had massive rendering bugs and no CSS2 support. They only fixed the worst stuff five years later, with IE7. Of course web developers still had to wrestle IE6 for years after that, as its market share declined only slowly.