After first finding them in high school a decade ago, I've been re-reading Allen Steele's Coyote trilogy recently, and I've been struggling to figure out what the author means to reflect on the American Civil War and the Confederacy. I was hoping to start a discussion about it and see what others think.

Reading a very surface-level interpretation, the book follows a group of hardy separatists from an oppressive government, headed by a brave and wise captain Robert E. Lee. They manage to homestead and succeed on their own, independent of the United Republic of America, until suddenly the Union comes around to enslave them and ruin their independent way of life. Along the way, they've managed to discover a race of intelligent monkeys, while implicitly extolling the virtues of the hardy settler, the explorer, and the individual unwilling to submit to the herd.

And yet, read with a little more unbiased perspective, the books tell a wonderfully compassionate story of people coming together to overcome common challenges. The main characters are rich in spirit and kind, guided by principles of moral good. The main villains are portrayed as either short-sighted or reluctant flawed people, or just flat-out inhuman machines. The world of Coyote itself is harsh but tamable, providing a backdrop for a tale of shared human triumph.

While I read it, I couldn't shake the feeling that the various allusions to the Civil War were some sort of Confederate apologia, but the themes of the book, and the persistent compassion that characters share seems at odds with that idea. On the other hand, why did the author name the wise captain Robert E Lee and set him and his band of individualist refugees against the Union, unless there was a purpose to the name?

I'm a little lost on how to analyze this, any help would be appreciated, even just discussion would be useful in helping me iron out my feelings towards it.