The main problem with IE, regardless of how good it is, is that it is windows only. This was true of all of Microsoft's stuff (particularly crappy mac versions don't count) (I also wasn't a fan of Mac OS 9 ... but there was bsd and linux for a number of years by then...) They used their own formats, which were not publicly documented or even really designed. If you had to use any single Microsoft thing, you practically had to use it all. Samba and later OpenOffice changed the situation but were really a lot of reverse-engineering and bug-for-bug-compatibility work, and of course Microsoft kept moving the goalposts with new versions and new bugs.
The resentment comes from the lock-in. You had to pay a lot of money and deal with licenses (or pirate and deal with cracks) just to experiment. You had to deal with the surprisingly flaky file sharing and dhcp client etc. You had to deal with the fact that there wasn't a good terminal or shell, that the compiler was not trivial to download and install and invoke from a script, etc. If you have the freedom to choose the "convenience" of the Microsoft user-oriented products or not, it's not such a big deal that Microsoft everything sucked for networking related development. But if the lock-in gets you somehow, you really resent it.
EDIT: and I almost forgot! microsoft calling linux a "cancer", funding lawsuits over linux kernel code, trying to make it harder for linux to support ACPI based systems - more underhanded lock-in to their crap