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.