According to this article, 6.7% of vehicles in the US are sold with manual transmissions. It's barely a market worth considering by some automakers standards.
The US may not like MTs but the rest of the world (Europe, Asia, etc.) is far from going clutchless anytime soon.
However, many manufacturers continue to show automatics as "optional" at an additional cost of $1500 or so.
Some manufacturers may offer manual models to lower their starting price. I noticed that Kia (and others I'm sure) is offering some of their base model in manual only. If you want to go automatic, you have to upgrade to the next package and pay 4-5k more.
2011 Kia Sportage LX (MT only) = $23 895
2011 Kia Sportage EX (AT only) = $28 895
It's great for buyers who are in the market for a stick shift but it must be a shock for someone who assumes its an automatic ... like most (95%+) CUVs on the road.