Just want to start off by saying, the movie looks like every movie I watched in middle school and high school. Stories might all be different but you could tell me they were all using the same set of costumes and I wouldn't have trouble believing you.
Not really knowing any of the history of the characters the cast is based off of, I find it difficult to understand why Aguirre holds so much sway over everyone. When he overthrows Ursua, the promise of the possibility of riches really shouldn't be enough to pull everyone to him so fast, and nothing he's done on screen should instill the level of fear needed to do so.
Even if you didn't know from the start that everyone was completely fucked, the tone of the movie doesn't exactly hide anything. At no point in the film do you ever have a feeling that anyone is going to do anything except die. Technically, Aguirre doesn't die... but dude is dead. If nothing else he's going to trip over a monkey and break his neck on a log.
There's also a couple of scenes that, I'm honestly not even sure if they were meant to be comedy or not. A group of people sitting around counting, and after one gets his head swiftly removed it continues counting and says 'ten'. Or another person, exclaiming that 'The long arrows are getting fashionable' shortly after he finds himself with one protruding from his body. It's like a Python sketch tried breaking out during the movie.