[discostu]

There was nothing anti-military in the season finale, or the show as a whole. The president said "stand down" so they did. The military answers to the civilian government because that's how things are supposed to be. Even if the civilian goverment is wrong they still run the show. People voted for Baltar because Baltar promised they'd stop running, after living in tin cans and fleeing for their lives for the last 6 months the pople were tired, it was the wrong decision but it was their decision.

[Little Ray]

Sorry, some elements of the show are totally silly.

You don't run from a genocidal enemy with 47k+ refugees; you militarize 'em, incorporate 'em into the forces. You don't have elections, you have staff meetings. You don't worry about the treatment of genocidal war criminals (aka Cylons), you worry about military discipline (you don't get to mistreat 'em 'cause of military discipline - just kill 'em - or vivisect 'em for research). You don't let malcontents run off with valuable hardware (like ships), you shoot their leaders, toss the rest of 'em into brig and let 'em work it off in the penal brigade. At worst, you move 'em off to some low value units (not the mining and manufacturing ships...) and send 'em on their way.
Oh, and you don't shoot up hundreds of advanced Cylon raiders when you can capture 'em and salvage or reverse engineer 'em.
And how is it that Cylon skin jobs can interface directly to a fiber-optic cable and the Colonials STILL don't have reliable test for 'em? Seems like there should be some very obvious physiological differences...

As I said, I'm really only "up" through the end of season 2 ("Pegasus"), but really don't like the writers. It IS better that the old BSG, but, from what I've seen so far, the writers have issues.