Humanity was fighting the flood, and since their worlds were being infested, they were forced to expand into forerunner territory. The forerunner, not knowing about the flood, got pissed off at the humans and said "Get the F off our land" and decided to decimate humanity. Humanity however eventually found a cure to the flood. But just as they did, the forerunner killed them so bad they were sent back to the stone age.
Then once the forerunner discovered the existence of the flood they were like, "well F***, not only were the humans good people after all, but now the flood they were dealing with is our problem, and we just blew up the cure!"
So forerunners choosing humanity to continue their legacy was an obvious choice. Partially because they had created a flood cure before, what's to say they couldn't do it again? And partially because the forerunner were saying "sorry we went to war with you over the completely wrong reasons and sent you back to the stone age, if we give you some of this cool stuff can we be friends again?"
Of course, no thanks to the covenant, the flood were forced upon us hundreds if not thousands of years before they should have.
[Edited on 03.02.2011 10:49 AM PST]