While twitter bootstrap does help give websites a familiar layout for users (ie. nav starts in top left of header, login/account functionality in top right), I agree that without customization, it's helping to make the visual web more like eating vanilla paste.

I made http://convertunixtimestamp.com/ over the weekend, and I used bootstrap mainly for the responsive design. But I tried to customize it enough so that it wouldn't be recognizable as a bootstrap site.

And I chopped about 85% of it out b/c it just wasn't needed.