There's also probably an ego play, too. I see the "Objective-C isn't that hard. Learn it." argument a lot, but it does have a steep learning curve. For one, it's syntax is confusing if you don't recognize the brackets and messaging. Second, it's a lot closer to C than something like Ruby or Python, so you have to learn about types and memory management.
It's a mistake to compare these frameworks to native apps, not that you did but several posts are. They are different, and that's good. It's like complaining that C isn't object oriented. Find the right hammer for your nail.
One of the points in the article is that the second you want something phonegap doesn't provide, you're stuck back-peddling, or over-engineering your fix. We've already come across such a situation with one of our upcoming projects that requires camera overlays.
Ultimately, it's important to compare options, whether they be frameworks, native, or toolchains. They're all avenues that need to stand their ground against other avenues.