I think people
should configure Bootstrap and use different colours, and approach it not as a strict guideline but as a good starting point with useful widgets to play with. I am, however, completely happy with people using Bootstrap unconfigured, it looks good and for the most part is normally used in a really clean way. A lot of iOS apps look like the stock components, and that's fine as those components are nice and clean.
There often seems to be a bit of push back about websites looking the same, especially with Bootstrap sites, but we don't expect (and often don't want) applications running myriads of different UI styles on our desktops. Maybe it's just a sign of the times.