Considering that Mobile Safari has access to lots of confidential data (eg. iCloud keychain), and runs in a less restricted sandbox (can make data pages executable), that's probably the last place where Apple wants to try out some new technology.
EDIT: It's weird how iOS is now arguably the most secure mobile platform, after all the shit they got from Blackberry in the beginning :)
Security problems were pointed out to the WebGL guys a very long time ago and continue to be pointed out - they have not all been addressed (for whatever reasons - i don't want to imply that any of them are impossible to resolve) although extensions exist or have been proposed to resolve the more serious concerns.
This is quite well documented: http://www.khronos.org/webgl/security/
I'd be more inclined to think that Apple don't want to include WebGL for other reasons though. Their track record with technology is much less than encouraging...