The demise of manual transmissions is mainly due to lack of demand. And it's not just in heavy duty pickup trucks: They disappeared from passenger cars and heavy duty earthmoving equipment decades ago. And a lot of heavy and medium duty trucks are sold with automatics.
It's true that a lot of folks never learn to drive manual transmissions. But which came first, the chicken or egg? No way to learn to drive a manual when there are very few stick-shifts on the road.
Interestingly, manuals are still very popular in Europe. Cars almost identical to those sold in the US are available with manual transmissions in Europe. Partly this is due to high fuel prices in Europe (never mind that modern autos can match or exceed the mileage of manual transmissions), but mostly it's just a mindset: proper cars come with manual transmissions. It's just a reversal of North America, where market demand is for automatics.
There's really no big advantage in operating costs between a manual and automatic transmission. True, overhaul costs for an auto are high, but replacing a heavy-duty clutch isn't cheap either. Fuel mileage with a six-speed overdrive automatic is likely to match a five-speed manual. So it really comes down to the driver's preference, and pulling a heavy load over hilly terrain with a manual tranny is brutal work. Personally, I'll take six speeds plus a torque converter over five speeds and a clutch any day.