Yes, the religious themes are somewhat understated, but they seem to run through the film at various levels. I'm not at all personally religious, but I think the deployment of certain religious metaphors is really very evocative and effectively done in BBM.
My favorite (maybe) is the three crosses that signal the beginning of the film.. they're of course, really electrical wire posts that appear to the left in the screen as the semi-truck carrying Ennis pulls up in Signal.
Also, as Lynne indicates, there's a long, complex argument to be made about the idea that Jack is a "Christ-like" figure. He is always the one leading Ennis (physically and visually... he's in front of the flock of sheep and even as they walk to the bar at the beginning... Jack is leading Ennis). Also, Jack does "walk on water" so to speak (a literalization of the song he sings) when they're on the way up to Brokeback and need to cross the stream. Jack is the one seen walking through the water. Etc. There's also the idea of Jack as a "sacrificial lamb" (the seeming connection between the sheep killed by "predator loss" on Brokeback equated to both Jack and Earl) that may be seen as playing into this metaphor too. Further, at the end... the idea that Jack is capable of comforting or reaching out to Ennis even after Jack's dead (i.e. through Ennis finding the shirts) seems to extend this concept.
And, the fact that Ennis and Jack are shepherds (even though we usually use the more modern phrase sheep herders or ranch hands) is of course loaded with possible religious subtext.
