Unpopular? In some designer circles maybe, in 90% of working web developers absolutely not. Not to mention that the flow layout techniques are sub-par and worse than tables in every area where they overlap.
It's no coincidence that the w3c finally created a grid layout spec as well as the flex layout to surpass the "flow" mess, or that all desktop UI layout tools use some grid and/or constraint based system for layout.
Plus, content-presentation separation should be at the level of CMS/database/RESTful service where the data come from, not imposed at the level of the published content.
I agree that html tables are used and get the job done, but I would much rather deal with one container div, one 960 div, then 3 section divs for header, content, and footer, then, one or more tables doing the same thing.
It's 2012, and CSS is easy. With a little work, all the problems you can point out can be fixed easily, including flexible grid layouts, and columns, responsive design. Can you even make a flexible table layout?
Also, every site I maintain that uses tables for layout, uses more than one, and it's source is absolutely horrible. While you say that a CMS should level should handle this, that doesn't factor in responsive design, site creation, or massive overhauls to style. Semantics will be an important element in the web soon, and doing html tables for layout, is considered wrong by anyone who cares. http://www.w3.org/2002/03/csslayout-howto
