>That means they have around 59 times more than that amount in cash, not the 200 you claimed
Still, same order of magnitude, and still many times over their app profit.
>Also, I think its telling that Apple themselves mentioned App Store Sales as a main factor in their revenue earnings for Q4 of their 2014 fiscal year.
Telling towards what?
I don't see how you can justify being off on your facts by 3-4 times by saying its still in the same order of magnitude. You overestimated their cash on hand by about 422 billion dollars. Again, I see the cash on hand as a weak argument. What really matters is how much annual revenue and profit it brings in. Apple is going to be concerned about anything that adds or takes away from their revenue in a significant way.
Its telling that App Store sales are a significant source of revenue for Apple. One that could possibly justify not making improvements to Safari that could make it better compete with native applications.
As others have mentioned, there are other benefits from native applications, like vendor lock-in, which Apple isn't going to get with web-based applications.
[1] http://money.cnn.com/2015/01/28/investing/apple-cash-178-bil...
[2] http://www.apple.com/pr/library/2014/10/20Apple-Reports-Four...