First of all, in Prometheus, it was David who woke up an engineer, but the engineer directly killed everyone present except Elizabeth. However, if you read the deleted paragraph, the engineer and David had a brief argument, which shows that human beings are useless to them. Moreover, black water is really used to destroy mankind. Engineers actually extract some creative human beings from their own genes for a certain purpose.
They want someone to worship them and work for them. Finally, there may be several reasons, one of which may be dissatisfaction with human beings. Director ridley himself said that engineers look at the species they create every once in a while, and if they gradually feel out of control, they will be destroyed. Moreover, in the process of the appearance of alien contracts, it is obvious that the racial dress of engineers is very backward, which seems to be the result of lack of resources.
Secondly, it may be because of the internal reasons of the engineer family. Just as human beings have inner struggles, perhaps the engineers who created human beings also have inner struggles. The reason for this struggle may be that human beings are out of control, or as mentioned above, they are fighting for resources and living places.
Then there is the purpose of weapons manufacturing. If it is to destroy mankind, then weapons can only be said to be human experiments. Imagine, if engineers strive for more living space and living resources, will they be satisfied with destroying only human beings? Maybe they will continue to destroy the intelligent life of other planets after destroying mankind, so this is the first war of weapons experiment for mankind.
Another suspicious character in the movie is David. After being made by human beings, this guy really saw enough of human greed, especially because his maker wanted to live forever by looking for aliens, which made him very despised. After flying to the engineer planet, he first tampered with the wine, which proved that he had consciously eliminated these companions.