There are "smart" content management systems like Movable Type that let you type into a text area using "bold" and "italic" buttons like Word. When you submit, it automatically converts it to HTML.
The NYTimes designers, apparently, type everything out by hand and inject the HTML directly.
That article says nothing of the sort - it says that the designers and IAs (who are presumably the people who build the site "templates") hand code their markup, but it makes no claims about the content producers who are actually posting up stories on a day-to-day basis. They certainly use a CMS, but there's no indication of whether they author in HTML, use some kind of WYSIWYG interface or use some other form of markup.