I think the main point against analogies is when they are used as proof for the situation they are being compared to.

I'm not versed in formal logic, but I believe it would be:

"A -> B", and I want to prove that "C -> D"

So I make the analogy that "A is similar to C, and B to D in some ways" thus then C -> D"

A lot of people will take this as a valid proof. But it has yet to be proven that A and C, and B and D are actually interchangeable.

Edit: To refer this back to the original argument, saying that the AppStore is like a brick and mortar store, and Cheerios is like Epic games is a nice analogy, but it can't possibly prove anything because they are just not the same thing.

What they may do though, is potentially align the reader's point of view with the writer's, but not necessarily towards the _right_ point of view, assuming there is one.