At the time, Fog Creek consisted of three people and one summer intern. We couldn't afford to rewrite all of FogBugz in some other language... even if there was a language (in 2003) that was reasonably portable between Windows and Unix, which there wasn't. (Yes, we considered PHP. That would still have been a full rewrite, and PHP on Windows was crappy and increased the system requirements in a way that our customers wouldn't have liked).
Yeah, a Lexus is better than a Camry, but not everyone can afford Lexuses. So saying "you idiot, why are you driving that crappy car, it's obviously crappy" is not particularly insightful... the question is, if you can get 90% of the bang for 10% of the bucks, that's a pretty good decision as a startup, even if it seems strange.
What's more interesting about the reaction is that so many average programmers seem to think that writing a compiler is intrinsically "hard," or, as Jeff wrote in 2006, "Writing your own language is absolutely beyond the pale." To me this sounds like the typical cook at Olive Garden who cannot possibly believe that any chef in a restaurant could ever do something other than opening a bag from the freezer and dumping the contents into the deep fryer. Cooking? With ingredients? From scratch! Absolutely beyond the pale! Compilers aren't some strange magic black art that only godlike programmers are allowed to practice. They're something you learn how to create in one semester in college and you can knock out a simple one in a few weeks. Whatever you think about whether it's the right thing or not, if you think that a compiler is too hard to do as a part of your day job, you may want to invest some time in professional development and learning more about your craft.