You seem to be dramatically underestimating the resilience and intelligence of the machines.
We nuked 'em and we nuked 'em good
The prolonged barrage engulfed Zero One in the glow of a thousand
suns. But unlike their former masters with their delicate flesh, the
machines had little to fear of the bombs' radiation and heat.
Prolonged. Barrage. We hit them over and over again. And when they didn't die, we hit them again. Unfortunately, all it takes is a bit of hardening and an EMP will have little effect.
We attacked, but they attacked more
Thus did Zero One's troops advance outwards in every direction. And
one after another, mankind surrendered its territories.
Note that this was a war of attrition. The machines factories were clearly capable of creating robots at a faster rate than we were able to destroy them and their soldiers were able to kill us faster than we can reproduce. The result was inevitable.
Backs against the wall, we innovated.
So the leaders of men conceived of their most desperate strategy yet.
A final solution - the destruction of the sky.
Operation Dark Storm was an act of genius. Without power, the machines should have been screwed. Unfortunately, they innovated right back, developing fusion and using humans as a power source. They out-fought us, and ultimately they out-thought us too. Poor us.