I think Aguirre is prejudiced in many ways.He has met Jack before, but presumably not Ennis, yet he treats Ennis with the same disdain as he does Jack.He is rude, curt and scathing to both the boys. I always thought he looked down on the boys as he considered them beneath him in every way.They were presumably less educated than him.
He probably had his suspicions about Jack's sexuality. Yet as with many things in the film and book, he is a study in contradictions.He sees Jack and Ennis on Brokeback, and he does not immediately send them packing. So although he appears to be very prejudiced he shows a degree of tolerance there.
Back down from Brokeback he is rude and abrupt with them both again.
Maybe BBM changes all who venture there, bringing out the "real" them, or the better version of them. Or maybe Aguirre was just the same as Ennis, a gay man in denial.In general we despise those who we see as reflections of ourselves.