Yes - the problem here is multifold:
Companies want to be seen to be on the iPad. They also want a walled garden to their content - so the Amazon app will keep the user on Amazon - there won’t be the temptation to use that Google bar to find cheaper prices elsewhere. In essence, iPads (and tablets in general) are tempting to companies because of this.
At times, an app is better than a website. I fond the FaceBook website harder to use on an iPad because it has not been built for a touch interface. Links are too small, some behaviours of the website are better with a mouse than with a finger. Because of the way Mobile Safari displays content, scrolling in certain situations is bad. I also don’t want to keep pinching to zoom text that I can’t read properly. So I use an App (and as there isn’t a Facebook iPad app, I have a third party one). Ditto the x404 web site - I use Tapatalk.
The Moleskine app is a mess. It looks good, but I’ve not used it since loading it onto my iPad - it’s complex. I agree with the article on that one.
As far as I can make out, iOS (and indeed any tablet) scream “keep it simple, stupid” - yet too many app developers seem to like to add complexity.
I can name few apps that are simple to use, and which take advantage of the touch interface. I would like to single out ComicLIfe - that app feels like it was really thought out before they started coding. There are a few niggles, but it shows how a complex app can make things quite simple.