Is there any specific criteria regarding the choices in naming? Was it in acknowledgement of their prior service to the U.S.? Wouldn't their service against the Union have given cause to not give them an enduring legacy?
Always thought it slightly odd and figure there has to be more to it then "We pulled the name out of a hat."
There are a couple of reasons.
The Confederate Army still to this day is held in high regard, with many of its generals (none more then Lee) considered excellent leaders, with their campaigns still studied today.
Most of them are in the South anyway, thus there is going to be a lesser degree of possible resistance.
Some werent founded by the Army. Fort Bragg in NC for example from what I recall was founded by the state to rain men in WW1, and was only then taken over by the Army after it was named.
They have loal meaning. Besides already being located in the South, they are usually relevant to the state. Hence why Forts Lee, Bragg, and Hood are in Virginia, North Carolina, and Texas.
So you really have men who are still held in high regard by the modern Army, who might not always have named the place, and who might occasionally seek some political good will from the locals.