The Guild Navigators are terrified of Paul. He possesses the ability to destroy the only supply of Spice in the known galaxy and due to their dependence on it, they're utterly unwilling to go against him.
"The power to destroy a thing is the absolute control over it. You've
agreed I have that power. We are not here to discuss or to negotiate
or to compromise. You will obey my orders or suffer the immediate
consequences!"
In the subsequent books, his total dominance of the Spacing Guild leads him to one military victory after another since his troops now have total freedom of movement in space (at zero cost) whereas his enemies are now confined to their own planets unless they can come up with monumentally expensive spice bribes.
To quote from the book:
"Stop playing the fool," Paul barked [at the Emperor]. "The Guild is like a village
beside a river. They need the water, but can only dip out what they
require. They cannot dam the river and control it, because that
focuses attention on what they take, it brings down eventual
destruction. The spice flow, that's their river, and I have built a
dam. But my dam is such that you cannot destroy it without destroying
the river."
