So I completely agree that using this (and most other CSS frameworks) is going backwards a bit in mixing layout with HTML. But I actually always did that. I just wish writers on the subject would help me not be confused by starting out by admitting that they are not following the notion of layout done in CSS.
Some people posted on here that Bootstrap is just for getting quick prototypes done, and then when things are stabilized, you should switch over to semantic, properly separated CSS. But if so, is that the intentions for all grid based CSS frameworks?
Using divs with classes of row, column, span_X, grid_x, et al. is, from a semantic standpoint, no better than using tables. And Bootstrap's CSS file is nearly 2500 lines, unminified with a 47K minified file size. That's a lot of overhead if you only need grid, typography and pretty forms.
It makes a lot of sense to keep the full CSS file linked while iterating the design/layout, but once it's in production, the grid classes can be replaced with semantic names and the extraneous styles removed. Here's an article I found on the 960gs homepage that covers not only combining/renaming classes, but also minimizing the amount of extraneous container divs: http://www.webdesignerdepot.com/2010/03/fight-div-itis-and-c...
A div exists to have no meaning. Using it for layout doesn't hurt anything except page size (unless there was a more specific element that you could have used accurately instead).
I don't understand how we're in the year 2012 and people are still repeating these "rules" without any understanding of why they might matter.
Consider this example based on the Bootstrap examples - you have three boxes containing stuff within a DIV with a class of 'row'. At some point in the future you decide to turn this into a column. Easy to do in the CSS - just change the width to the with of one item, and they'll stack on top of each other. BUT, now you have a column labelled 'row' in your HTML. This is a fairly simple to rectify example, but this problem is pervasive in grid systems.