The RAW here is quite clear:

"Computer Illiterate provides a –2 dice pool modifier to all tests that involve a computer, electronic device or Matrix-connected system in any way, shape or form."

But I can't help thinking it's not the RAI. How would you rule on:

Driving a car "by wire"? It's still "an electronic device" by a strict definition, but the computerized parts aren't being manipulated directly by the user. Would a penalty still apply? Would one need to use entirely manual controls to escape it?

Using Cyberlimbs? They're obviously computerized, but the input comes directly from the user's central nervous system. Would computer illiteracy really impede someone's ability to run with cyberlegs?

Using a gun with Electronic Firing? It's electronic in that it uses wiring and electrical jolts to trigger the primer. but it's "an electronic device" nonetheless. Would a computer illiterate gunman take penalties?

Just looking for a little feedback here, 'cause if we take the RAW literally, it seems a bit too onerous for +5 BP.

I'd say it only applies if you need a computerized interface. Anything that's used by simple mechanical operation doesn't get a test, unless you're interacting with the actual computerized components. You can drive a car, but you can't make the mp3 player work. You can use the cyberarm, but you can't make heads or tails of the maintenance display. You can shoot a gun, but you can't get its remaining ammo display on your AR. To take an absurd example: you can wear underwear, but you can't store your e-mails on it.

I would agree with you. I would even go as far as to say you can't drive a car by the wire without incurring the +2 modifier (as your interacting with a computer interface). Think of it this way, someone who is completely computer illiterate (take your grand parents as an example) can't understand anything that isn't at least mechanical and as such wouldn't (and may be afraid) know which buttons to push. As such stuff that is a computer in the background and doesn't require the character to make a test to use the computer portion of the device (example: Cyberware) then wouldn't occur the +2 modifier.

One interesting idea that 4th ed brings to the table for computer illiterate is the second crash.

It's entirely possible that an individual could be computer illiterate when it comes to anything related to AR or the second crash but perfectly comfortable using electronics from the original matrix. Maybe they don't buy the idea that the matrix 2.0 is in any way more secure than the original, maybe they were just too old to relearn everything.

I could actually see a small to moderate sized group of neo-luddites who continue using stuff like decks to interface with the new matrix, after all a deck, like a comlink is really just an interface device. They could be modified to accept the new architecture and the like but still rely on wires and the like to get the job done. The same group could even continue to provide goods and services (legal and otherwise) to people who aren't comfortable with the matrix 2.0. They'd be tiny by comparison to the number of people who adapted (think something like the Linux community now days) but they'd be there.

My opinion on the Comp Illiterate Flaw (written the same in 2nd and 3rd) is that any time that you're going to use a computer or electronics based skill, you get the penalty. If the skill you're using is Firearms or Drive or whatever, this penalty should not apply.

How I deal with it as well...

I see the core problem with how people think. Untrained people can still grasp computer concepts quickly, but, my mother, for example, who has a Ph.D. and while sometimes ditzy and forgetful, is very intelligent. She does not, however, think in metaphors. I do. I haven't spent much time learning the details of computers, but I understand how computer interfaces work more intuitively. I pick up functional computer skills quickly, and I am self-taught at expert levels on a few software packages, mostly because I know how and where to look for answers, and I am not afraid of deleting parts of reality. My mother wants step by step linear instructions for how to do most things with the computer. From there, she learns the steps, and gets things done.

(I was quite amused when I found myself explaining that "software" was not the floppy disk. It was on the disk, much like text is on a page, without actually being the page. Of course, she started to get lost when I used the metaphor of the book.)

A computer file is not a "file". That is merely legacy terminology left over from the business world that found a use for computers in mass quantities. There really is no file. There is the computer language string of binary code, and the graphical interface that we use, and a few layers in between, but the graphics we see are merely metaphorical images. To say, "The file is downloading" is very much like saying, "It is raining cats and dogs." There are no animals falling from the sky. Nor is there a file coming down from anything.

Mechanical technology doesn't involve metaphors. A plow literally plows. A wheel turns. A lever can be pulled, and the chain of interlocking parts can be observed to its conclusion, whether that is setting the emergency brake, or opening a door.

As I noted in the example with my mother, intelligence is not necessarily a factor in thinking metaphorically, at least, not in the abstractions of Shadowrun game mechanics.