At the beginning, the cylons (at least the dove party) wanted to coexist with the humans, but unsurprisingly the humans did not trust them and started attacking the cylons.
This caused the cylons to face a difficult choice:
Just plain extermination. Not what you would expect from a "dove" party.
Control the humans remotely (keep the human camp contained, don't mix with them). Safer for the cylons, but would make the cohabitation process take longer (which maybe was a good idea). It would risk more radical humans taking control from Baltar, which could lead to a frontal confrontation afterwards. Also, the humans could end up dying anyways due to Baltar's incompetence (more on this later).
Control the humans with help from the less anti-cylon faction. The human police would purge the violent element and after that the two races could coexist. Failed when terrorists began targeting the human police, which in turn helped radicalize the police force.
Non-violence: just tolerate the human attacks and keep resurrecting. Even if resurrection is at hand, the cylons consider dying an unpleasant (at best) situation. If they allowed it to happen, the dove party could lose power to the radicals. Also, the humans knew that the cylons would resurrect anyway, so the gesture would not mean as much as it would had it come from other humans. Finally, it is possible that this option was simply not in their nature.
Leave the humans undisturbed. This option was not possible, as it was mentioned several times that the cylons feared that letting the humans alone would mean that, in the future, once the humans had regained their strength, they would attack again (and the cylons would no longer have the advantage of infiltrators).
A point to consider is that the humans were in terrible shape when they arrived at New Caprica (in part because the planet was barely habitable, mostly due to Baltar's incompetence), so maybe the cylons chose a more direct approach in order to sustain the colony.
Another possible influence could be the cylons' mysticism. Once they had decided that God wanted them to coexist with the humans, they were interested in learning why.