Although I have seen a few Bootstrap sites, I have only just started to look into it seriously and I was quite shocked by what I saw in the HTML - loads of nested divs with multiple classes attached to each.
In the old days before CSS, people used to decorate their HTML with fonts, colours, etc., and this was considered a "bad thing". CSS enabled the HTML to be very clean and free of styling information. This is "separation of concerns" which is considered to be a "good thing".
Although the styling in bootstrap has a level of indirection (i.e. it references class names rather than directly specifying colours etc.) it is basically putting the styling information back into the HTML instead of using CSS as it was intended.
Don't get me wrong, I have written enough CSS to know how difficult it is to maintain, so I can understand how bootstrap came about. My question is really whether bootstrap is seen as a hack for people who want to knock up a site quickly and don't care about separation of concerns, or whether it's actually considered a good practice to keep the style information close to the HTML (which you could argue is a kind of encapsulation) rather than lumping it all together into a separate file (i.e. that CSS wasn't really the right solution).