I think the Cylons still pursue the Colonials because they want them dead, simple as that.
However they are plainly lack lustre in their methods - The destruction of certain aspects of Cylon property (the Supergun, parts of the Capital - remember, not an actual lot was destroyed, just rendered inoperable by the destruction of the control centre - and various basestars), may have been an inconvenience, but certainly did not inspire the Cylons to greater methods of searching did they? I mean, after the raid on Gomoray, the Cylons only sent one Baseship after the Galactica. Now if they were pissed off about the Imperious Leader being attacked, a capital being attacked and two basehips being destroyed, why continue the chase with only one ship? Surely more would be appropriate as the Colonials are now definitely a threat to contend with.
Going by the books and the television series, the Cylons want the human race destroyed, plain and simple, because they represent a threat to the Cylons ordered way of life. The books expand upon this greater than the series and can give you greater insights, but that is what I believe. There's none of this man versus machine rubbish, and no, the Cylon robots did not destroy their creators - please do not even go there (that is one thing I am not entertaining!). Knowing how inventive and creative the humans are, and knowing that they will not sit still, the Cylons have to destroy them.
So, the only other thing I can think of, is that the Cylons are obviously spread thin over a wide range of space, and are probably involved in other activities as well (like destroying all the human worlds the Galactica visits and leads the Cylons too).
The Colonials did not stop at Terra because it was not Earth. They wanted to find Earth, and John (the angel) gave them some directions. I also get the impression that the angels did not want the Colonials to stop there, but to give peace to the planet. You do not argue with angels.
However remember, where the Colonials go, the Cyons will follow. This means that Terra will very shortly be in for the fight of its life - after all, are not they human, and what is the Cylon order for humans?
Initially low. Would have to be. They left without stocking up properly on food and fuel, and then have the food was wasted. Later on though, if they can build new ships or find somewhere to repair, then they might have more. I think it will be a never ending struggle for fuel and spare parts though. When a ship explodes, it does not tend to leave much, so they would not go around savaging for old bits. Food shouldn't be a problem unless the population expands, which (hopefully) it will. So they will need more ships, parts and fuel. (That sounds a bit like the Monty Python sketch about the Spanish Inquisition, does not it?!).
At the end of "The Hand of God", The Galactic is left with an interesting decision to make. They are now at the end of their galacy. And this time, I actually do believe that the Colonials are at the edge of their galaxy, or at least, at the edge of a cluster.
However this poses some problems...
According to reality, galaxies are not that close to us - Andromeda, our nearest neighbour, is some 2.9 million light years away. Now, with that kind of distance, there is no way at all that the Galactica and her fleet will make the distance and survive. No chance at all. And if they can not make it, would the Thirteenth Tribe have been able to with Kobolian technology? Assuming that a hyperspeed journey is about ten light years (bigger than I actually think it really it), and assuming that each journey is about an hour, then regardless of all other considerations, a trip will take some 33 years... Not much hope of supplies lasting that long, is there?
However, we know nothing of the Galaxy of the Galactica. It may be that their galaxies are closer together than ours, but then they would still have to breach that gap when they go to it.
However... Galaxies are made up of spirals or clusters (well, some are anyway), so it is possible that at the "Hand of God", they think they are leaving the galaxy, but instead they are leaving one of the clusters or spirals... This would still take some time (although I have no real information on galaxy formations or internal distances yet, so any figure could be used here), and the space in-between would still be space...
This could also make the Colonies within our own galaxy, just maybe the other side. I mean, the Milky Way is made up of some 200 billion stars and the like, so plenty of space for everyone concerned! Our galaxy is also a cluster galaxy, so the above theory could hold out very well, and still not contradict anything.
...[Some research later]...
Apparently, outside clusters do lie some stranded stars. Now, whether these have planets are anything around them is impossible to tell, but for the sake of a good story, they might have, which would aid the Galactica no end, especially if there was life and supplies and stuff...?
The worst time would indeed be between the galaxies. The ships would have to stock up completely on fuel and food before they go, there would be no turning back at all, especially as the Cylons would pretty much figure out who destroyed their Baseship, which would mean reinforcements heading that way. Would the Cylons still pursue the Colonials? Absolutely! This would be the trickiest moment for the Colonials - they must go forward, but only when ready. Getting ready would mean stopping to restock and re-supply, but they only have a certain amount of time to do that.
However, whether they actually leave is an interesting question though. Based on all the above, I would not personally think that they could make it, not without some serious help. But then, the ship of lights and the 'angels' did lead them in that direction, so obviously someone had some hope for their success. I think they would leave the galaxy. It would be difficult, fraught with danger, rationing, and stuff like that, but after a few climatic struggles (the stuff TV series are made off), and just when things were about to get really grim, they would find the new galaxy, cluster, or star with planets and supplies.
Remember though, that the Cylons would also not have an easy time of it either.
Once through, they would have some breathing space certainly, but suddenly, the Colonials really are on their own. A new galaxy, new stars, new everything (except for the fear of following Cylons, who *would* come, but maybe not just yet, and certainly not in the numbers they had been with). First things would be to restock and supply, and who knows whether or not this would even be possible! Okay, so we know it has to be (it is a TV series after all, and the 13th Tribe came this way before), so that at least makes thing easier. As to what the aliens and the stuff are like, well, definitely a Star Trek Voyager approach now, but no going home!
No reason why they should. In the series humans are everywhere the Galactica goes because of budgety constraints and also the designers wanted us to identify with them. Also, it seems logical that the Colonials galaxy was filled with humans. Maybe these were all off-shoots of the Colonials or the Kobilans, or even splinter groups of the Thirteenth Tribe. We never did learn or find out if the Terrans were native to their world or whether they also were colonists. Maybe they were colonists, but destroyed all their technology and records and come to believe that they are natives. Okay, this does not hold too well if they have archaeology as a skill, but we have had worse things in sci-fi.
Or maybe it is like Star Trek: TNG where they find that all bipedal life evolved from one similar source?
In return for helping the Galactic destroy a Cylon Baseship, a deal was made with Baltar in that he would be stranded on a habitable world with supplies and short range communications.
How do we know that Baltar has in fact been let go? The deal was made, sure, but was it honoured? He might have been killed on the Galactica when it got hit, he might be on the Prison barge and forgotten about in the excitement, Adama might had faltered on the deal thinking that Baltar was the lowest form of scum and did not deserve the breaks (however I doubt that, Adama was most definitely a man of his word). What about the other crew though, would they just stand by and let Baltar go? Baltar, the man who sold out the Colonies... I feel a lot of bad blood there.
Apparently, there are two main views on the fate of the Pegasus. The first, held by some fans, is that the ship in the episode where Count Iblis appears, is in fact the Pegasus, which is why Apollo tries to hold Sheba back from the wreckage.
The second view (apparently voiced by Glen Larson himself) was that the Pegasus did survive and was going to reappear in the second series. I believe that one as well. In a time of bleak turmoil, it is always good to have some hope. Besides, this way, the Pegasus could return in times of need!
Of course, there is always a third view - that the Pegasus was actually destroyed when it attacked the Cylon baseships.