Agreed. Additionally, it's thematically popular that when part of the US military becomes the bad guy, it's usually limited to "those guys" and not the entirety of the Military. Typically "those guys" comes in the form of a well meaning but rouge unit, a General with a vendetta against an opposing force (i.e. hasn't gotten over the end of the Cold war), a traitor of some kind, an indifferent chain of command, etc etc.

These are things audiences will rally around. Behind Enemy Lines is an example[1].

[1] http://en.wikipedia.org/wiki/Behind_Enemy_Lines_(2001_film)