A computer is not removed because it is a computer, but because of the dense electronics that most computers contain.

I doubt your kindle will have to come out, I would put it on par with a PDA or PSP, neither of which have to be taken out for security.

As it stands, (and I can't vouch for other airports) shoes don't need to be in a bin, you can place things to the side of your computer in the same bin, also, you don't need to remove the laptop from any nylon sleeve it may be in -- there's no point, especially since people usually place the laptop on top of that very sleeve.

I've had a few kindles come through, and the only extra attention they got were my questions about how it stacks up against a Sony Reader (what I have, and what collects dust).