I've found two reasons for this in the more than a decade since I got my first PowerBook. There's two things: there's always a few hardware features that come at a premium, and the mac stuff has some hardware niceties that I like regardless of what OS I'm running.
Everything comes and goes in cycles, feature parity is always shifting around.
For example, when I got my first G4, comparable PC laptops didn't have:
- target disk mode
- a widescreen IPS display
- gigabit ethernet
without getting really expensive.
When I got my first intel mac it was:
- dual link DVI
- a backlit keyboard
- a builtin camera
On my current macboor pro, which I bought about two years ago it was:
- thunderbolt and the ability to drive an insane number of displays
- that screen, when the first retina came out, that screen was unmatched
Laptops that had all these features have always come in at similar costs. There's sort of an 80/20 rule in play, and Apple just doesn't bother too much with things below the 80, but this seems to change a little more every year.
Also, I really love how my current MBP plugs into my display. One cable for power, USB, and display. The thunderbolt displays are basically a solid docking station.
If you dig the hardware and want some premium features (usually really current IO options) the cost makes sense to me.