I think the engineers wanted to wipe humanity out because of our destructive nature.. and the fact the dead engineer in prometheus was dead 2 thousand years it would give good indication that religion might have played a big part in it, the crucifixion of jesus, the romans, genghis khan, all that lead them to decide we were unfit for the life they gave us, also they might have been lead to believe we would eventually come looking for them and cause more destruction to them since we are a hostile race, to them anyway we seem to be. Since prometheus took place in 2093 i figure that 2 thousand year mark is a good reason why.. we were very war hungry and stoning people, taking over countries, we were not worthy of what they done for us.