The stylus is, like, the HTC Flyer's main "thing," no? Why sell it separately? I don't get the logic behind this....

Because you can still use pretty much all of the functions without the stylus and not everyone will need it. It's also a good way to save a penny if you're only interested in the tablet part without the stylus. I do agree, however, that it's pretty annoying having to buy accessories separately in many other cases (i.e. usb cables with new printer purchases).