I tested it on Android, and its WebKit also lacks programmatic focus on input elements. Didn't test the ontouch problem. Mobile Firefox does the right thing.
The funny thing is I intend to package my app in native wrappers and distribute on both App Store and Android Market, so Apple does stand to make money. But, they still lose exclusivity, and it's unfortunate that they have a strong disincentive against improving HTML5 as an app platform.
I dont mean to comment on your situation specifically… I'm simply pointing out you're at a disadvantage:
1. Mobile Safari isn't feature complete
2. Apple has no incentive to make it feature complete
Think about it, Facebook, one of the largest photo sharing WEBSITE has a native app. Why? Because you can't upload photos on iOS.
iPhone OS 2 comes out, native apps get a full SDK with supporting frameworks. The browser gets "touchStart" events.
Apple simply doesn't want people writing browser apps because they dont make money nor lock users in.