If it's crap ... We'll tell you
They think they're underdogs.
They were fighting for more than just slavery. They were fighting for their own personal sovereignty.
Also some people have family connections, like their great great great whatever fought in the war, or something.
Lastly, some people don't like darkies.
It all depends on what you mean by "glorified".
For the most part, the reason that the south ends up being glorified in the film is due to a few issues of "stereotype" characters. Someone like Josie Wales (and most recently Bohanon from Hell on Wheels) are the ones who get glorified because they are out for some kind of "personal vengeance" mission after loosing their family. They become that "angel of death" to bring righteousness to the people who think they could get away with murder/rape because they simple had no one to answer to except for that ONE guy who has a shroud of death/immortality around them until they fulfill their mission of revenge.
There is also the "bad-ass-loner" type. These are the ones that are normally seen as the characters that have "lost their humanity" and became someone who can/will kill without remorse for some "noble" reason that only makes sense to that character. They are defending some small town, or one family, or even just one person in general. These characters are often seen in movies where they are trying to justify the use of force to stop someone from abusing their power or trying to run-off someone from their land.
Finally, you have that "had enough" with war type character that has already seen the horrors of war and being on the "loosing side" just doesn't want to ever fight again. Of course, this is until someone pushes them too far or kills "someone innocent" that pushes them too far. These are the ones who seem to be the characters that have just enough "fight" left in them to do one more mission (even though they would rather not do it) because no one else is able to face what they have to do.
Finally, you have it as a background setting to have a character "loose everything" in their world. They will loose family, or property, or their lifestyle. Mostly this is done to bring a character to their "breaking point" so that they can rebuilt their life and eventually bring some kind of self-assurance to the character other than just "living by status"..... Gone With The Wind is a good example of a character "loosing everything".
But mostly, it's all about using the Civil War as a means of presenting a once "normal" character that has lost everything, been through the horrors of war or seen as a looser... Without having the "benefits" of winning the war to justify all their actions. It's a cheap gimmick, but normally an effective one. Especially when it's done right, that's when you get such memorable characters AS Josie Wales, Johna Hexx and others.
A large part of it is that everyone likes a good underdog story. Also, at least in westerns, they always have those characters who fought for the Confederates in their past, to give those characters some edge or sympathy. Generally they were soldiers who fought and lost everything, and moved west for greener pastures, but their time in service haunts them or influences them. They lost their fight but will never back down from whatever fight lies up ahead. Also, to not alienate the audience, it is more a duty or sovereignty reason for why they fought to sidestep the issue of slavery.
These characters show up a lot, such as Mal in Firefly (a space version of this trope), John Carter of Mars in the Barsoom novels, Jonah Hex, etc. If you watch Bonanza or Gunsmoke enough you see these characters crop up a lot with various degrees of morality. Some refuse to believe the war is over, and others let it haunt them. Shane had that one minor character who let his pride and lost cause kill him. There is a lot of drama to be mined from characters who are fighting or fought for a lost cause.
I think the reason it shows up a lot in our media is because it is sort of a twisted American Revolution. We all glorify the Revolutionary War as our ideals won against an invading force that sought domination, but the Civil War was an example where a faction of American ideals lost. Also, since as a country we are fairly self centered, it allows us to root for an underdog from ourselves and thus can sympathize with. I wouldn't say it is glorified too much because we have movies like Glory which glorify the North and its ideals.
Gone With The Wind (both book and movie) don't glorify the Civil War South; they abhore it. They glorify the Antebellum South (the Pre-Civil War South). A big difference.
Second, The Outlaw Josey Wales doesn't glorify either. The movie doesn't get caught up in the notions of 'North v South' so much as Wales' family was (and later his unit were) killed by Union troops and he wanted revenge. The Civil War is mainly background for an outlaw's actions here. It glorifies Wales as a rebel, but doesn't really glorify the South.