Well, security doesn't seem like a big issue to me. It's there for iAd, so it's there, which negates any worries Apple has about it's security from what I can tell. I do think it's somewhat App Store related, although, I don't think it would be a huge issue. If anything, Apple could still sell access to / display ads on some sort of App Store/WebGL hybrid or section to the App Store. Coders could write code that could be accessed freely, or, if they deisred, submit it to the App Store and earn money. On Apple's end, they would provide the App Store, and either sell access to a restricted site, or, as many free apps do, Apple could stream the iAd to the site and the coder would benefit from being able to code for all platforms from one codebase. If a developer isn't concerned with development for other platforms, they could continue to, or also, code using the iPhone SDK. One thing to consider here is the disadvantage to WebGL are online access. Sure, Internet access is fairly ubiquitous, but if you're in a sub-terrain stucture, or some large building, or in the middle of nowhere, you can still find yourself in places where there's no online access. Conversely, iPhone apps can have full functionality without online access (given that it's doesn't require online access... i.e. Youtube.)
Just some thoughts...