Team America makes more sense when you understand that it was just supposed to be a parody of Jerry Bruckheimer movies. The reason the political satire has this very muddled view of "Bush era American military interventions are bad but also good but maybe kinda bad unless not" is because that's not the main thing it's making fun of.

Edit: That wasn't a defense of the movie to be clear, and I think Team America fails because it can't commit to making a point. It invites you to laugh at how crass and stupid the whole post-9/11 Bush era American ethos was, but it mostly seems to agree with the underlying premises that birthed that ethos, except sometimes when it doesn't. If the South Park guys wanted it to be just a movie parody then it shouldn't have any political satire at all, but it does, so it winds up as a satire that doesn't say anything. A movie like Airplane is much more successful as a movie parody because there's virtually no political content in it.