I honestly don't think the Engineers were ever happy for the humans, at best they probably tried to turn us a bit more civilized, Humanity was kinda like a surprise babby that they couldn't straight-forward eliminate out of some sense of responsibility, but once we killed one of their messengers (Jesus at the year zero; sent to try to teach us lessons) they had enough justification to kill us.
They still felt responsible for us though, so they basically gave us a chance of survival so long as we never developed space-faring capabilities, and did so by seeding the world with rockpaintings and art of one of their "nuclear silos".
The reason the ship in Prometheus was heading for earth was because of their weapons mis-firing on themselves, and they realized that any humans heading to this planet would die out too quick to return to earth to finish the job - so they set course for Earth, hoping to release the goo straight at the source.
The engineer in the movie was just straight-up pissed that their plan had failed, and that one of their "children" had the audacity to demand life.