Parts of the program may be running one process, but using many cores - that's hyperthreading. And you will see acceleration from that with both physical and virtual cores.

Aside from that, you can enable multiprocessing, which launches multiple copies of After Effects in the background, assigning one copy (process) to one core. This particular trick needs physical cores to actually do any work.

(And to put other minds at rest: AE CS6 has not changed or lost anything in this regard compared to CS5 et al. We're just trying to clarify what's really going on underneath the hood, so people can make informed decisions about hardware purchases. Feed your real demons, not your imagined ones...)