Their numbers are actually a bit optimistic. According to the EPA, only 3.5% of MY2013 cars were sold with manuals (unlike the article's 5%) and manual transmissions now have no fuel economy benefit (versus an optimistic 15%).
http://epa.gov/fueleconomy/fetrends/197 ... r14023.pdf
However, on a site like this, it appears like there are more manual drivers than there actually are. And (based on a recent Autoblog article) manual transmission cars make up around 20% of press cars (more than 5 times what they make up of the new car market). There is undoubtedly some social/PR benefit to offering manual cars, although they are unlikely to be profitable with declining sales numbers and no price premium. Development of vehicles for global markets will likely keep a few models available here for at least the near future.
But with no performance or fuel economy benefit and limited marketability, manual transmissions are likely to continue to decline overall. However, I think there is hope for a few holdouts. I would think about it like analog music versus digital music... they still sell records to an enthusiastic few, but sales are not what they used to be.