There is a very deliberate, functional reason for this use of noise: it obscures banding in fine gradients.
Gradients have become incredibly popular within flat design, largely due to Apple's focus on them since iOS 7. Apple uses extreme gradients, mostly. By extreme, I mean there's a lot of colour shift in their gradients, so they can avoid banding, mostly, by the combination of the angles they use and the amount of colour shift.
For more subtle gradients, particularly radial ones, a banding becomes visible, often, because there's not enough gamut to prevent banding unless using huge (48bit) colour spaces. To obscure this banding, there's various ways to increase noise, both chroma and black and white, and blend it with the gradient. This hides the banding, somewhat.
When done subtly, the noise isn't consciously visible. But you're starting to see it, which means you've noticed it and can't un-see it, and/or you're looking at examples where stronger noise was required to obscure the banding in the gradients, or you're seeing images where the noise is desirable and accentuated.
