story identification - Sci-fi book where humanity is rebuilt on a new planet after being wiped out

Between 2005-2008, I entered a Barnes and Noble and came across a book in the New Releases section that I regretted not purchasing. I remember only the following from the back-panel summary of the book:

Humanity was more or less wiped out.

The remains of humanity were put into a deep sleep on one (or more) large spaceship(s).

When they arrived a new planet, they had a society where religion was/wasn't outlawed (can't remember anymore).

A lot of bad stuff went down after humanity rebuilt itself on this new planet.

Answer

While it is earlier than your described 2005-2008 timeframe, there is a book published in 1999 by Stephen Gould entitled "Helm" (It's entirely possible it could have just been mis-shelved by a patron).

The TV Tropes website gives this synopsis:

Shortly after the conclusion of a war that destroyed the Earth, rendering it uninhabitable for generations, the survivors in the grossly-overstretched lunar colony decide to send four thousand in a colony ship to a planet that had been in the process of being terraformed. However, the colony ship was only designed to carry one thousand — and the other three thousand replace the supplies that the colony would have needed to start on the new planet as a technological civilization. The colony will survive ... but they will survive as a low-tech civilization that will have to rebuild to a higher level. And to help them, they will begin the job implanted with a strict religious code, designed to maximize the probability of the colony's survival.

The book actually starts much later than the colonization, but everything in that synopsis fits your description.

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