After driver's ed, the first car I used regularly was a no-frills 1979 VW Rabbit with a manual transmission, so I'm very comfortable with it (though I haven't owned a manual auto in several years).
It's not a big deal to learn unless you're a brand-new driver, IMO. Especially if you've ridden motorcycles, then you already understand the necessary relationships between the clutch, brake and accelerator. I taught an adult friend who had never driven stick before, and he had it down in an afternoon. All you need is some time, patience with yourself, and an empty parking lot.
I believe driving stick gives a feel for how the car runs. Makes you more cognizant regarding traction, fuel economy and stuff like that, even if you're piloting an automatic transmission. If you live in a city with a lot of stop-and-go traffic, your left leg will become very muscular.
Sometimes, in urgent situations, I occasionally find myself stomping the floor of the car with my left foot while braking with my right. Old habit dies hard, I guess.