Hi Kent,
The bootstrap skin has some of the container panels turned off so they only render their contents and not the divs. The custom css class would be added to the container div but since it is turned off and not rendering the custom class is also not rendered.
Changing it is very easy, in theme.skin:
<portal:OuterWrapperPanel runat="server"
RenderContentsOnly="true"
/>
change that to false and it will solve it for the blog and probably other features, just can't remember if they all use the same panel but I think they do.
For background on this see also the article A More Flexible Set of Container Panels
Hope that helps,
Joe