The technical reason is that the version of Chrome used by the WebView is older than the current Chrome app. As I recall it was old enough to miss the point where we started enabling WebGL by default on capable mobile devices, which is unfortunate but that's the reality of hitting a release date. :P
The good news is that the next time the WebView gets updated (I don't know the timeline) it should pick up the WebGL capabilities. There may be other reasons to disable it at that point but I'm hopeful that it will make it through unscathed.
--Brandon