What was the point of the *spoiler*
Pathogen. I can understand them wanting people to leave the pod alone, but if the aliens where actually nice then something that eats flesh and kills people and plants seemed a bit harsh.
You ruined it!
I thought it was explained quite well in the White House cut scenes.
It was a pathogen the aliens carried that they were immune to but most/some life in earth could not cope with. It wasn't intentionally aimed at humans.