Hard to say if they will stay or go. Some stats here:
Blog Post | Stick Figures: The Last Days of the Manual Transmission | Car Talk
When I went to look at Rangers in '09, the dealers had automatics only. One Toyota sales a-hole told me I really should buy an automatic. No sale there. GMC and Chev, Nissan and Toyota (other dealers) all had 5 speed trucks with no BS or "upsell" attempts. So I think there are still plenty of folks who see the "value" in the driving and long term ownership experience of a manual trans.
On the other hand, automatics are so much better now, at least for the first 100-150000 miles, and who can row through 8 speeds as fast and smooth as a computer?