Of course, nothing is preventing an independent shop from having their own free comic day in the sense that Reed described. It probably wouldn't be a bad idea; put it out in local media, you'll get your regulars in plus a handful of first-timers, they'll get a free book but a good chunk of them will probably pay for additional books or merchandise, and you might get return customers out of it.
This is of course very different from the idea behind the official free comic book day, where it is the big bad publishers footing the bill rather than the little guy.
^This. The point of free comic book day is to bring in new readers by eliminating the cost barrier for a single day. By putting out bullshit like the first section of Spider-Man Season 1(which I picked up, and hated) they are cheating themselves out of money in the long run, and many potential fans out of a lifelong passion.