Why not? Apple also doesn't allow Flash, so the question is, why? Does Apple make money from Safari? Is there a technical reason that might preclude another browser engine?
My understanding was that they don't want to allow executing downloaded code that hasn't gone through the App Store review (such as JavaScript in web pages). I think they allow Lua for scripting in games, though.
So, basically, a 3rd party JavaScript engine is not allowed. I guess you could write your own browser engine that doesn't support JavaScript.
I guess Flash was not allowed for performance and security reasons (lots of vulnerabilities, right?)