"Don't use tables, use CSS!" was a big message. But CSS's tools for tabular layout were extremely poor and difficult to use, leading to much frustration. It was a joke how hard it was to create a simple responsive three column layout in CSS, a thing easily accomplished with tables and very common on the web. Getting that three column layout right seemed like black magic in CSS1.
It was, but in hindsight maybe the message needed to be elaborated more. Perhaps it should've been "Don't use tables for layout, use CSS!"
Besides that, CSS IMO accelerated more complex and visually pleasing websites, and arguably spurned on the Web 2.0 look. Unfortunately, due to the message not specifying the for layout bit, it took a while for many devs to unlearn that tables are bad – tables aren't, they should just be used for tabular data.