So, at the beginning of the movie, we have the scene where Shaw discovers yet another cave with drawings, all pointing to star charts, pointing out there must be some kind of off world connection between all of their highly unlikely connected groups of people.
Her third or fourth line in the entire movie is:
I think they want us to come find them.
This is entirely based off her own personality and nonscientific bases. (Played off however, on the idea she's a scientific authority. because she was digging in rocks in the middle of no-where with a team)
Our next scene with Shaw comes from David being a creeper and watching her dreams as a child, talking about life and death, and the belief of God and higher planes, Shaw is constantly seen wearing her cross through out the film.
Our next speaking role with Shaw is during the briefing scene...Here it is explained the tall beings pointing to the star clusters drawn between each civilization must be aliens that came to earth....here they conjecture, through scanning and mathemagics, this system does exist, with a single planet with a moon, blah blah blah.
Thats Mr. Dr. Scientist Mans explanation....
Shaws lines, after being questioned by the cannon fodder are:
No, no, not a map, an invitation.
They engineered us.
I don't, but it's what I choose to believe.
Considering her religious background and her, based on pure belief, assumption that 'God loves us all' the Engineers being the obvious God/Creator reference within the movie...it's unsurprising she sees an invitation.
The rest of the film goes on, then we get to your scene. As pointed out earlier, she hasn't exactly had the best of days...
So our religious main character who thought God created us with good intent, has her b/f killed, gives a 'virgin birth' to a monster (she can't get pregnant normally) all because of the Engineers and their black goo..
She in her world view, can really only come to the conclusion, they must hate her.
She doesn't know they do, but she believes they do.