As @MrEntropy noted, the reason Haiku uses Alt is because the BeOS used the Alt key as the system modifier – much in the way that the Mac uses the Command key over Ctrl as well. And the reason I bring this comparison up is because on the Mac keyboard, the Command key generally sits in the same spot that the Alt key (Option on the Mac, where the Super key would be on a PC) does, which makes it a lot easier to use when going between the two (Be had run on its own hardware and Mac boxes/clones first, then Intel machines later). Also, the other advantage of this is that in the Terminal, for example, there’s no conflicts over key bindings (like having to press Ctrl+Shift+C, etc. on Gnome, KDE, and so on due to this dilemma) as it ‘frees’ up the control key to work on its own.
All that said, however, I can see where getting Ctrl switched around is annoying if you primarily use or prefer it. In the classic BeOS, you could change the modifier key from Alt to Ctrl in Menu preferences, and in Haiku, this has moved to the Keymap preferences, where it’s possible to “switch to Windows/Linux mode” with the press of a button. (And as a bonus, it’s also possible to switch Command to Ctrl on Mac OS 10.3.9 and up, although it might make using it a bit awkward).