Given that the Guild controls all interstellar travel, why don't they entirely control CHOAM?
It's pretty clear that CHOAM is basis of the wealth of the galactic nobility (beyond what is available to them on their respective planets). CHOAM can only conduct trading activities with the co-operation of the Guild. It would follow that CHOAM (and the nobility generally) should have no leverage against the Guild, given the very limited needs of the Guild (only spice, and the materials and fuel for their craft, and foodstuffs).
Consider also that because the Guild controls all interstellar transportation, any "naval" or military action against them would pit sub-luminal transport, and forces collected from individual star systems against the forces the Guild could amass.
This would leave them free to seize Arrakis if they so wished; it's not clear whether they could, or would even need to fight any other conflicts, given that they move faster than anyone, so would not require any garrisons for defence, only to maintain control of their planets.
Certainly in Earth history, the pattern is clear: the various European Indies Companies would assume complete control of the transportation of cargoes within their spheres, and in so doing, achieve a trading monopoly*. Why would the Guild not do the same thing?
note: * Ganted, this one sentence covers about 50% of the history of European aggression against the rest of the world, but I think it is sound enough for the purposes of this question.