I love the controversy...
With just over 100,000 ratings, Prometheus seems to be doing quite well on IMDB, with a 7.6 rating. I don't think the perception that it wasn't well received by the audience is reality.
I'm not sure what any of this has to do with individual people here saying they didn't enjoy the film, but whatever. As I said, I have no problem with others enjoying it or preferring the lack of explanation for certain plot elements, I just don't like people making broad-sweeping judgments about those who didn't like it. Nor do I like such judgments being made about people who did enjoy it. It's irritating that some people can't seem to handle the subjective nature of film enjoyment.
The crew are not military, so there is no reason to expect them to bring weapons any more than it was for the Apollo 11 astronauts to.
I would have no problem with them being willing to accept the risk of going on a first contact situation without weapons in order to appear benign (though that's not really the Weyland Corp. way, hence having the guns). Lots of scientists are willing to risk their lives to advance our knowledge of the universe.
That being said, the comparison to Apollo 11 where there was no expectation of extraterrestrial contact whatsoever is a poor one.
Let's look at this too...for one thing, a biologist wouldn't be fear free just because...they're a biologist! If you were surprised by human-like intelligent bodies you might get a shock yourself...but if you came up to a living creature, one that seemed like a harmless small animal, and it's your field, you might act a little bit different. The only real problem is that the biologist didn't go back AFTER being scared and investigate an obvious intelligent alien lifeform!!
I agree with flcat also, Steve Irwin got a bit of a surprise with a manta ray didn't he?
Of course being a scientist doesn't eliminate fear.
But if you're willing to hop on an at least four-year mission with unknown classified objectives for a corporation that sees you as overhead more than a human being, all while riding in brand new stasis pods in a brand new ship using brand new propulsion technology overseen by an android with no emotional attachment to your well-being, and then are perfectly willing to follow the natural selection-rejecting faith trumps peer review scientist on an expedition into the giant skull temple from Hell and take your helmet off thirty seconds in, maybe seeing a dead body shouldn't be that scary?
He shouldn't have been too surprised by human-like dead bodies since by that point they had already been briefed that they were looking for human-like inhabitants (actually 100% human according to the movie, but somehow giant and blue-gray and suddenly able to walk around without a spacesuit on planets with atmosphere poisonous to humans if it's the end of the movie and he wants to kill them real bad). Also, there was no welcome wagon, it's a desolate planet, and it was over a millenia since any contact had been made with them, so the Engineers being dead should have been considered a distinct possibility before they ever left Prometheus.
Also, Steve Irwin wasn't a biologist. He was a wildlife expert to be sure with decades of personal experience from childhood, but the whole point of his show was for him to get up close and personal in dangerous situations with animals to make the show more interesting and entertaining for viewers. Unless Millburn was filming the world's most long-delayed reality-TV wildlife show, playing snake charmer just for fun with the unknown space cobra in an obvious threat display has about zero to do with being a legitimate biologist.
But if a trilogy (or even a sequel) didn't happen, Ridley also wanted to frame things in such a way that the answers were right in front of you - you just had to bring your brain into the theater with you and "read between the lines." 
