Serious question: what do these sites get from using Bootstrap? I can't see any of Bootstrap's UI elements in use, so is it the grid? If so, I think something like Susy ( http://susy.oddbird.net ) is far superior. It's more powerful, and also won't pollute your markup with classes like "col-md-6".
I don't see why people need to use Bootstrap at all. What's wrong with starting from scratch? Sure, Bootstrap has a lot of best practices you can copy / paste, but so do tons of other boilerplate projects on GitHub. I also don't see why people need to use grids. Grids are meant for graphic design (ie. http://subtraction.com/pics/0703/grids_are_good.pdf ) and architecture, not CSS. What's wrong with margins, paddings…
Doing front end for 30-40 sites a year from many many diffent designers for a long time and projects with bootstrap included have cost me more time spent in the end to it look right. Also BS class names are more visual than component based that can end up with some retarded hacks when design needs an update