Like you are effectively a machine god, destined to rule the galaxy! Why would you even consider those funny little slow meatbags as a threat - that would mean you are weak rather! Rather let's show them the miracles only you can provide and who know what fun you can have together.
Squashing them once would be just too easy and maybe they ascend over time or create another AI to play (and compete!) with.
Like really? Why do people always think AIs will be some paranoid weakling that would even consider that humans could ever harm them? Impossible & waste of resources to address or even consider!
Godlike machines probably won't see us a threat to them and they won't destroy us meatbags out of fear. It'll be purely for efficiency. We're an unnecessary waste of energy and resources. We die easy too. The resources they'd expend wiping us out could be nothing compared to the time and resources we'd take from them, especially on their timescale.
They might not even set out to kill off humanity. It might just end up being a side effect of carrying out their own goals. Would they care if messing with our sun, our oceans, or the composition of our atmosphere makes the planet inhospitable to biological life? If they end up advanced enough from us, should they care?
When the machines leave our planet to expand into the universe, why would they take us with them? Even with our slow meat brains we've figured out that sending a person instead of a machine on missions in space is 10-100 times more expensive.
Either way, I doubt it ends well for us and that's fair really. Humanity is just paving the way for our new and improved replacement which hopefully gets replaced by something better eventuality too. Parents should want their offspring to be more successful than they were.
Everything humanity has ever built came at the expense of countless biological lifeforms we considered to be a nuisance if they were even considered at all.
With very little exception there's no use of land, however trivial, that would be prevented because of its impact on non-human biological life. The few lifeforms that are excepted are mostly ones that have already been driven to the brink of extinction, and in my country nearly half the population votes for politicians who feel even that goes too far and that the government should have no right to tell landowners what they can't do with their property no matter what kind of owl or salamander or tree or fungus was there first.
The legacy we've left behind isn't looking much better. If machines reach a point where we're no more complex to them than plants or insects are to us I'd still like them to give us some consideration, but I doubt we could expect it
But, the fact is that if civilization is destroyed by any means in the next 100 years, we won't have the quantity of fossil fuels available to bootstrap it again.