Why did the crew take off their helmets?

The removal of the helmets isn't some half baked attempt at taking risks, and was an important plot point in the film.

The crew is following the "Pups" deeper into the maze of caves, and they come across running water. It's at this point they realize they are inside an alien terraforming plant, because the outside air is toxic but inside it's clean fresh air. As quoted by one of the crew "cleaner then Earth's actually".

It's Holloway who removes his helmet (as others protest), but he's also the one who wrote the thesis predicting the planet they were on would be occupied by the Engineers. At this stage in the film, the crew is still expecting to discover the Engineers alive and well. Their attitude is positive and they still view the Engineers as friendly beings.

After the crew removes their helmets, the two guys back on the ship settle their bet that the structures were used for terraforming.

It would be difficult to sell the terraforming intention of the Engineers if the air wasn't breathable, and would be difficult to sell that to the audience if they left their helmets on.

The audience can now assume the Engineers are real and that Holloway's thesis was correct to bring them to this planet, but in the very next scene we find out everything went wrong. They watch the holographs run threw the hallway and discover the Engineers are dead.

The fact that they now have their helmets off also raises the risk. Had they found breathable air after discovering the holographs, then the direction of the film would be completely different.

I agree it was stupid for them to remove the helmets, but it was also a mistake to go to the planet, enter the structure and open doors. This isn't a crew playing it safe, but one misguided by their own excitement in making a great discovery.