Bootstrap's strength is that you can use to to quickly build a uniform, fully functional, cohesive and clean UI.
Just because you can, it doesn't mean you have to.... and just because you don't have to, doesn't mean you shouldn't. It needs to be evaluated on a per-project basis, like anything else we do. Some tools and services really call for a custom look. Some, let's be honest, just don't.
I see things like internal tools being a great example of when to use Boostrap's defaults--that web app to visualize analytics on your data, your ticketing system, that private web interface you built for your Git repositories, the documentation manager, etc. Use Bootstrap, be cool with it, free up your designers and creative energy to roll out custom layouts on your client-facing pages.
In fact, just yesterday I wrote a blog post about my thoughts on using Bootstrap in "production": http://www.projectorpm.com/blog/2012/03/10/dont-hate-twitter... (FYI, the blog and the product are both built using Bootstrap)
They linked this: http://lesswrong.com/lw/2pv/intellectual_hipsters_and_metaco...
Once I got past the vague offense at thinking of someone calling me an intellectual hipster, the point sunk in and I tried to move on.
http://blog.jenius.me/post/18909693841/to-bootstrap-or-not-t...
http://blog.jenius.me/post/17162410587/stop-using-bootstrap-...
I'm still not sure if I would use it in a 'production' application though (perhaps with a lot of fiddling to the default styles).
As a side note has anyone else found it funny that a few months ago anyone submitting a project to HN that used bootstrap would get comments like "awesome using bootstrap", "bootstrap is the new standard for the web", etc. And quickly the sentiment is turning to "yuck another bootstrap site" and "learn some css you fools".