The argument that WebGL "competes" with OpenGL-ES, to the detriment of Apple, makes very little sense to me.

You only need to look at the number of engineers Apple has contributing to WebKit & new web standards (CSS transitions & animations, WebGL etc.).

On the other hand it's a serious feature of their iAd business.

As an iOS developer I feel that native apps will have a technical edge for a while. WebApps are built with tools that weren't designed for creating GUIs, you can do it but it is much less efficient and effective. This is especially true for complex applications like games (the ones that would benefit the most from webGL).