I'd been wondering about the AL and FL flags as well--the MS and GA flags are/were the only ones to directly incorporate the Rebel Flag post-Civil War (ca. 1890s and 1950s, respectively), so far as I know. Georgians voted in 2003 to change their design to one which no longer incorporates the Rebel Flag (though it is largely based on the first Confederate national flag, i.e., the original "stars and bars"); Mississippians voted down a redesign which would've eliminated the Rebel logo in 2001. In both cases, large numbers of voters either boycotted or simply blew off the referendum.
I understand and appreciate that Southerners who are enamored of the Rebel Flag (pretty much invariably white folks in my experience, and I grew up in a 90%-black Delta town) don't view it as the equivalent of a bumper sticker saying "I long for a return to slavery" or anything like that (and yes, I realize most of their ancestors weren't slaveholders either). In fact, I'm pretty sure I remember being taught in grade school that the inclusion of the Rebel Flag in our state flag was meant to commemorate our war dead and their kinsmen who suffered on the home front, which doesn't sound particularly noxious so far as it goes. But what about the suffering and death of black Mississippians--nearly 40% of the state's population even today, and far more before segregation sent them northward in droves looking for a better livelihood? The full civic realization, to the extent that it ever existed, of the Southern values many fondly see embodied in the Rebel Flag--states' rights; chivalry; an agrarian "yeoman" ethos; cultural refinement as opposed to "plebeian" culture; community-focused civic and religious life, etc.--was heavily built upon the blood, sweat and misery of black slaves, there's simply no getting around that. Not all black Mississippians I knew actively or chronically chafed at the Rebel Flag's ubiquitous presence, just as not all chronically chafed at the ubiquitous racial slurs and monopoly of whites on local political power--but I can't recall a single black friend (and most all my friends were black) who felt the kind of pride in or identification with that flag that some of my white friends seemed to. And of course there were those who regarded it as I might regard a flag which incorporated a swastika.
For that reason I felt ashamed when Mississippians voted down removing the Rebel logo from our state flag, and despite my appreciation of all the good things the Rebel Flag symbolizes to many, I feel the same way about people flying it in their yards or wearing it to school in T-shirt form. Personally, I don't care nearly as much about the "separatist, treasonous" sentiments it allegedly conveys towards the US as a whole--as I've said before, I reject the notion that Southerners, regardless of how they feel about the Rebel Flag, have any difficulty identifying themselves as Americans first and always; and in view of history, I can't say I find the argument that white Northerners might feel marginalized or oppressed by it all that compelling, though I can understand why the descendants of those who died fighting for the Union (and against slavery, that being the root cause ultimately) might take offense on those grounds. Now the defensive analogy to how Native Americans might feel about the US flag, and what untroubled short shrift that gets, that I can understand, though not as a justification for flying the Rebel Flag really--but then Native Americans, at least in principle, are sovereign nations in their own right; African-Americans are not.
