The humans had a war with the Forerunners before the Flood attacked. As punishment, the humans had all their technology taken away, causing de-evolution. That is reason enough for the Forerunners to hate humans. 343 Guilty Spark even seemed to think that the humans and Forerunners would fight. He seemed especially worried about the humans meeting the Didact.
"And without the Librarian around to temper his rage, well, these Reclaimers might almost prefer the Flood." -343 Guilty Spark