It's very odd, yeah. Prozac isn't even one of the more common medications they give you for AS.
It's useful for both depression and anxiety disorders, and it's entirely possible that the doc thinks you may have one or both of those; but if I were you I'd be asking more questions-- like why'd he prescribe Prozac for Asperger's, when it's been shown effective for depression and anxiety disorders?
Asperger's shouldn't really be medicated unless there are comorbids that respond to meds. There really aren't any meds for having a different sort of brain wiring. I guess you could make a case for stimulants; but if you benefit from those, you usually have enough traits for an ADHD diagnosis anyway.
Yeah, go to that doctor and ask about why he prescribed Prozac. Either he prescribed it because he figured you had anxiety/depression in addition to AS, or he just prescribed it because "hey, it can't hurt," in which case, why bother taking it?
Did he refer to a therapist? That's the usual treatment for AS--basically, education, teaching you how to do stuff that AS makes harder to do.