Was it sitting at Helena Regional or in-flight? It looks like the primary carriers that fly out of HLN are Northwest, Horizon, Big Sky, SkyWest, and
Comair. Of those, the only one with a predominatley red color scheme is Northwest, however only a few of their
smaller aircraft are all/mostly red. Did you see what kind of airplane it
was?
I doubt it was a military aircriaft, I think they would probably go with the more common white scheme if they were trying to remain inconspicuous.