If the Cylons are sentient and by default more intelligent than humans, why didn't they just attack Caprica and the colonies and let the few survivors leave? They could have owned the planets and started a full civilization. But by following Galactica and the other surviving ships they constantly sacrificed themselves for no real reason other than hatred. But aren't they of higher intelligence? They pretty much do to the humans what they themselves hated about the humans.
Intelligent people let emotions blind them all the time.
I don't see why intelligent machines would be any different.
On a separate note, however, did all the Cylons follow the refugee fleet? I seem to remember seeing Cylons on the planets in a few episodes. Sending a detachment to destroy a fleeing enemy makes sense; live enemies can regroup or find allies or develop technology that can destroy you, dead enemies can't.
Nothing says they're unemotional.
We never see the mechanical Cylon units expressing a great deal of emotion, because they don't have much range of expression. Considering they were sentient enough to fight for their own freedom, and then push their own sentience by creating human versions of themselves (with help), they have at least some emotional drive beyond cold logic. At least one unique raider ship ("Scar") was also shown to be particularly vicious, although this could be interpreted as extremely effective tactics. The prequel series Caprica never got completely off the ground, but what was seen implies their initial sentience is based on a virtual copy of a human mind, and no more capable or immune to faulty reasoning as their human masters.
They were heavily influenced by the twelve human-type Cylon models.
The human-type models - who are at multiple points shown to be just as flawed, emotional, and more or less as intelligent as the humans they are pursuing - are shown to have a ruling council that guides the course of the Cylons as a whole. In theory there's a democratic vote system in place, with each human model having a representative and getting a vote.
...who at some point shackled them all again.
Late in the series it is revealed that the mechanical Centurion units have had inhibitors installed to suppress the sentience that led them to independence in the first place. It's not revealed exactly when this was done, but it calls into question exactly how much control the robots ever had over the course of the war, and paints the human-type Cylons as just like the humans they are trying to exterminate. When these inhibitors are removed, they promptly and predictably start killing their slavemasters, and these free Cylon are the ones by the end of the series willing to simply go find their own way and leave the surviving humans in peace.
...and one of those twelve had massive daddy issues.
Model One / Cavil was pursuing his own agenda, and is implied to have manipulated the other Cylons multiple times to get his own way. Cavil massively hates that he is an imperfect human-type, and his primary motivation is revenge on the original five human-types from Earth that helped the Twelve Colonies Cylons create their own human-types like Cavil. He views the attempted genocide on the Colonies as punishment on the Five, and is shown arranging various scenarios as mental screw-yous to his primary parent figures. His douchebaggery may well be responsible for the entire series, although he certainly wasn't the only one who hated humans, or he wouldn't have had anyone to manipulate.
The metal-Cylons were held like slaves by the human-Cylons. So don't expect to much from the metal-Cylons. The human-Cylons however changed their mind multiple times. They are a very young "species" with a lot of questions. And their hierarchy is not strict. Usually they followed whoever had the better arguments/influence. One of their biggest goals was to find their "soul" and be able to reproduce. The fear of being "just a machine" was very strong. So they were basically between: "destroy the enemy and eliminate everyone forever before they strike back" and "the humans have souls and can reproduce, we want to be like them".