Re: OS wars aside --
The difference is those repositories are not money sources. So you'll not make money from look-alikes or other scams. It may also be more difficult to get into those repositories with unknown applications, and anyway, you'll reach a limited number of users - the "app stores" front ends are designed to lure users into installing more stuff, unlike repos where you usually look for something you already know.
But as seen in other articles, other repositories, like the WordPress one, are being used to deliver nasty code.