In the USA, cars must be certified to meet emissions and safety standards set by the US Government. A standard transmission car, for purposes of certification, is a separate model and must be certified separately from the same car with an automatic transmission. That's expensive, and if the manufacturer doesn't see enough of a market for standard transmissions to offset that cost, they won't offer it.
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This is a HUGE factor, and likely the most significant.
There was a time, probably still is, when the heaviest tow ratings on pickups came with auto transmissions. Not because they were stronger, but because most people did a crummy job of driving manuals. They lugged the motor on uphills, shifted like a monkey with a hammer, and did not downshift as needed for some downhills. What I see now is that most folks who buy a pickup for towing get one that is too light for the boat or RV (the one tons are the threshold minimum) they want to pull, and make it worse with a ball hitch instead of a 5th wheel.
Commercial trucks: I was driving when the first automated transmissions came around, and like any new product, there were a lot of problems. Never drove one. The only truck I could stand to drive with a 10speed (generally not enough gears) was a Mack Superliner with a V8. It had the torque to overcome the lack of gears - grab 10th and drive 1000+ miles without downshifting expect to change roads or pull over. 6% grades, miles long, 78K, no downshift. I much prefer the 13, 'cuz you can drive it like a 9 and only split gears if needed for weird grades and such, except the 444 cummins I drove a bit had to be rowed around by the shifter. Fast, but no powerband.
There are two types of automated transmissions. Some have a conventional clutch, so 3 pedals. Some have a centrifugal clutch (2 pedals). All of them are actually manuals transmissions, but they are controlled and shifted by computer. The mechanical lockup is better than the slushbox/fluid lockup of a true automatic. The reasons that trucking companies go with the automated transmissions do include the lack of skill of newer drivers, plus a recognition of the safety issue having fewer distractions. In addition, with a modern computer controlled automated tranny, the engine performance characteristics and gear choice are better matched. Serious operators are measuring mileage to the 3rd decimal place, and when running 110K+ miles per year, especially in fleets, the $$ start to matter. If I was speccing one now, I'd likely go with an 18 speed autoshift, in part because of the lower gear selections for moving in tight spaces, and the flexibility of running in states with different speed limits. If I am able to do so, I plan to have an RV made on a Western Star, and it will have some form of automated transmissions.
We have two cars, my wife 2007 Outback, and my 2011 Legacy. We had a tough time getting hers with a 5 speed, but the additional control was a factor we wanted. Mine has a 6 speed, and with the additional gear gets 5+ better MPG on the open road because I am turning 800+ rpm less. (For no reason I can discern, 1st is taller than in my wife's car, which is unfortunate.) I do well enough with it to exceed the rating on the CVT, which is 4MPG higher than the rating on the 6 speed. That requires paying attention, and I more or less drive it like a Cat C15.
Most people do not pay enough attention to their driving, so an automatic serves them better. Living in crowded areas, an automatic is likely to be more realistic. My commute to the job I just left was 63 miles, with a total of 9 stop signs or lights, but mostly open. The 6 speed was glorious for that. With modern automatics getting more and more gears, so the splits are smaller and the top is higher, the mileage advantage is tipping to the automatics, especially if they are well tailored to the power band of the specific engine.
The only time I regularly drove an automatic was in a squad car. Given that there was a lot more to pay attention to, that was a good idea. Throw in rural LE where the throttle is often 2 positions (none, or full), and that made more sense too.
These days Honda use a CVT on their bikes. Look up CTX700.
