Humanity already had a strained relationship with the Forerunners. At this point in their relationship, from the Forerunner point of view (as seen in the Terminal 'War') humanity appeared to be invading Forerunner territory and destroying their settlements and ships completely unprovoked. Imagine receiving a message from an absolutely ruthless enemy who has already killed billions of your kind, telling you about how there's some kind of unstoppable cosmic horror on your world, and that you need to work together. No way you'd believe them. Especially since the claim is so ridiculous. Imagine if humanity did decide to contact the Forerunners. In the time it would have taken to convinced them of the threat, the Flood could have already taken starship(s) and headed to other worlds, or they could have overrun the planet. Or both.