The Cylons did a thorough job when it came it destroying the Colonies, but it was not total. It is known that at least one group of human refugees managed to escape, and at least one other warship was away from the Colonies and it too survived the holocaust.

When the main Cylon fleet arrived, they landed ground troops with orders to kill - not enslave or capture, but kill - and kill they did. With nothing now to stop them, the Colony worlds were doomed, and millions died. Human tenacity and stubboness meant that the job took a while, but the end result was never in doubt. The Colonials simply did not have a chance. Pluton radiation destroyed food crops and vegatation, water supplies were contaminated, medical supplies wasted. Aeriana found itself with no way to feed its teeming masses and starvation did what Cylon ruthlessness did not. Having no need for the same supplies as the Colonies, and having no desire to capture the worlds, simply destroy them, over time the Colonials left on the worlds were all killed.

Whether others escaped is unknown. Certainly there were some Colonial outposts that existed, and some light fleet elements on patrol were scattered around, but what happened to them is unknown.

After the destruction of the Colonies, the Cylons would certainly turn their attention to these other outposts, especially when they realised that some of humanity escaped. Rogue fleet elements would be tracked down (either by detection by Cylon patrols, or by information supplied by Baltar's spies) and destroyed by overwhelming numbers. Colony worlds bombed into pluton wastelands.

The outlook for humanity in the area formerly of Colonial Space is indeed very bleak.

What is fact though, is that one Battlestar, the Battlestar Galactica, escaped the destruction of the First Fleet, and managed to get back to the Colonies, before the Cylons started landing their death squads. There, Commander Adama, one of the Council of Twelve and commander of the Galactica, realised that life on the Colonies had come to an end, and there was no hope of remaining there alive.
So he sent word to all survivors who assembled in any ship they could find, and lead this fleet away from the remains of the Colonials and (hopefully) from the Cylons too in a quest to find the thirteenth tribe.

The historical archives are quite clear on the beginning exploits of this fleet, and thus we know that Colonial Man did survive to leave the galaxy and had many encounters on the way, battling Cylons, encountering Count Iblis and the Ship of Lights, locating the (presumed destroyed) Battlestar Pegasus commandeered by the Legendary Commander Cain, only to lose it again when it went up again three Baseships single handedly, locating new races (the people of the planet Terra), and managing to capture Baltar, the renegade human who sold out his race and teamed up with the Cylons to destroy man, although he was obviously tricked by the Cylons into believing that he would be able to rule the survivors.

But whether or not the fleet of the Galactica found Earth or other remnants of man is unknown.

Unfortunately, the wake of the Galactica leads to more killing. Remember that the Cylons want to exterminate the Colonials and the race of man. The Galactica's travels certainly led them to other worlds long forgotten by the Colonies and thus also to the Cylons trailing them. It would only be time before more Cylon ships and death reached them. When does this stop? Does it stop? The Cylons are known for their completeness, so maybe they will not rest until all the Brothers of Man are removed from the Universe.

The final chapter has yet to be written.