Sheer brutality was a tool they had not the slightest compunction about using as a weapon.
We are talking about a brutal era however. Where communications were limited and the best way a centralised institution could control a large empire was not to be everywhere at once [which they couldnt be], but to have local allies indebted to them and most importantly to ensure that no one ever wanted to attract their wrath - hence the examples they made of Spartacus and conquered cities.

I wouldnt consider the Romans to be especially brutal - they simply ran a large, expansionist empire in a brutal era. Should a citystate be defeated, their families would be enslaved, their lands and riches taken from them and they would vanish from history as an independant people. The Romans fought every war realising that this is what was at stake for them. Their Hellenistic enemies often did not truly grasp that. Romes manpower and wealth was only a factor in their rise, their true strength was that they were willing to expend them in great quantities to achieve victory. Their enemies often only wished to avoid defeat.

In terms of the era, when Alexander the Great caught up with Bessus, the pretender king who slew Darius he had him stripped, put in a halter and flogged whilst the entire army marched by, before he was mutilated [ears and nose cut off]. Then, still alive though clearly in agony he was sent to Hamadan for show trial and execution. This is a cultured Hellenistic monarch dealing with the realities of running an anceint empire.

Look at how Syracuse treated the captured Athenian prisoners after the defeat of their disastrous expedition to Sicilly - left in a quarry to die of exposure and thirst.

It wasnt a pleasant era.

They were dominated by Rome out of fear of reprisal, but held no love for the Roman state. The Social War is just the boiling point of centuries of simmering grievances.
True, but even when Rome was at its weakest point against Hannibal the bulk of its allies remained loyal even though it was routine for cities in Sicily to switch sides depending on which appeared the stronger currently. Obviously fear of Roman reprisal played a part, but cities that went over the Hannibal usually only went over upon the approach of his army, so the fear works both ways.

The Romans dealt harshly with subjects that went over to Hannibal but they also put effort into praising and rewarding the loyalty of those who remained solid - at least one unit of Italic allies were offered Roman citizenship for their efforts but turned it down, Capuan equites who refused to return to rebel Capua via a prisoner exchange deal were also rewarded. There was also their probably deliberate flattery of allies through the use of extraordinarii which can only have helped ensure the loyalty of those allies. Those who returned to the fold were also reprimanded, but often not punished as a captured city might expect to be.

Rome put an immense amount of manpower onto the field during the Hannibalic war, putting a real strain on their subjects and allies so in my opinion its not remarkable that some cities and some Roman troops went over to Hannibal but that so few did even when Rome was at its weakest.