From reading the blog posts of a few of the developers it’s pretty clear that the review team just doesn’t understand what it is or how it works. When asked why a web browser is allowed to download files and an app using wget is not they can’t give a satisfactory answer.
The most logically consistent argument they could make is that alternative browser engines are disallowed... so logically an implemntation of "wget" which is just a wrapper around the Safari engine should be OK.
Of course, all of this is arbitrary. Apple just wants to be able to control their platform, they don't actually care about having rules and enforcing them with any semblance of fairness.
It's unfortunate that developers have to put up with this. I say "have to" in that my understanding is that Android users (in general, present company likely excluded) won't pay money for high quality ad-free apps. So if you actually want to make something good and be paid for your trouble, it's iOS or bust.