One of the reasons manufacturers don't offer manuals as much as they used to is, from my experience, due to the fact that not many people buy them anymore. Automatic transmissions have come a long way since the 70s and 80s, and now in some cases offer better performance and fuel economy than some manuals in certain models.
One of the reasons you still see manuals offered on base models, is to have low entry price point to adverstise for the whole model line (starting at only $9995 for example). Once you add automtic, and a bunch of options, the price jumps to $14995 for example. So on paper the lower price looks way more attractive and drives people into the showroom.
There is some folks out there that do prefer manuals in loaded models, but from my experience working in the car biz (at Honda), the loaded model (Accord EX-L sedan with 5 speed) would sit on the lot forever until that 1 in 250 buyer came in and wanted to buy it. Another reason is that sometimes resale value is lower on manual tranny modesl than on automatics due to the fact that not as mnay people know how to drive stick, therefore when people are buying a new car they take that into consideration as well (whether they'll have trouble reselling the cdar later).
So to summarize your question, it's mostly supply and demand, as well as marketing that drives what transmissions are put in what models.
As for your Hybrid question, I belive that if you take a stripped down model and put a Hybrid premium on it, it will eclipse it's non hybrid counterpart with all the options and the pricing. Right now the Hybrids are treated more as "premium models" and in most cases those that have the money to pay a Hybrid premium also want to have all the bells and whistles.