That's partly a thing of volumes: the models that sell a lot go cheaper than models that need to be ordered specially for specific wishes. So, in the US, everyone assumes automatic and manual gearbox isn't any cheaper. In many European countries, manual shift is the norm and you paid a lot of extra for the rare luxury model with a weird transmission that eats a lot of fuel.
Nowadays, with DSG and other dual-clutch transmissions, the automatics have become more common also in Europe. I think my next car should be a Škoda Octavia with a diesel engine and DSG automatic.
Manual is still usually about $1000 less in cars where it's an option. Probably for this reason, economy cars are more likely to offer it than fancier ones.
I would think this pricing is more based on a commercial positioning decision than actual economics - the manual is cheapest, and it maybe has less options for other fancy accessories, so that there is a very cheap "prices begin at" option which few people actually want. The margins may be even smaller there because of the extra cost of specific models, but it makes sense to have these available because then the volume models can have a slightly higher sales price.
Previous articles I read on the topic said the majority of standard transmissions sold were in economy cars. If you're stretching to buy a new car $1000 counts.
Nowadays, with DSG and other dual-clutch transmissions, the automatics have become more common also in Europe. I think my next car should be a Škoda Octavia with a diesel engine and DSG automatic.