The cave paintings and pictograms suggest the Engineers had visited Earth many times since our creation, benignly checking up on us, but then 2000 years ago a ship sets off from a biological weapons facility heading for Earth loaded with, essentially, germ bombs. I agree it wasn't explicitly stated, but I took the inference as they meant us harm (and Shaw certainly drew the same conclusion).
But, it was the writer's stated aim to keep things deliberately vague precisely so we could counjoure up all manner of theories. That's why I liked the movie so much.

