People have religious views. This is true in the Alliance as well.
Overall, the Alliance started out as a pretty cosmopolitan society. The nature of the mission made this unavoidable. People had been drawn from all over Earth, from a wide variety of ethnic, religious, and cultural backgrounds to be thrown together on a single colony. Rigorous psychological screening left the worst fanatics back on Earth, and for the most part the main group was composed of people with a very “live and let live” mentality.
Some of the “hitchhikers” were a little more devout than the average Great Journey colonist, but none were anywhere near jihadi levels of fanaticism. Even the people who founded Sonoziel after being dumped unceremoniously from the decaying warp field were no more fanatical than any other church in a relatively secular nation.
For the most part, the Tau Ceti II colonists went about their business like people in any other good-sized city. They worked for a living, went home to their families, had hobbies, played games of all variety, engaged in social activities with their neighbors, and some of them founded churches and similar groups. Aside from the hardships associated with terraforming a planet with unbreathable air, life was good. Largely boring, but good. And good, relatively uneventful lives don’t tend to breed religious fanaticism without an agitator. So people went about their lives, practicing whatever religion they chose.
Things were a little different on the Lost Colonies. Most of the Lost Colonies were founded by monocultures. They had been sent by a single group, usually a government but there were a few religious groups as well, to promote their interests as part of the Great Journey mission. At worst, a few planned to settle some distance from the rest of the colonists to live in their own society. When they were encountered by Alliance scouts, the main difference was their lack of contact with other cultures, but it wasn’t an issue for the most part. If anything, these cultures added even more diversity to the Alliance.
There were exceptions, though. As every Alliance citizen knows, the most notable was the cultural insanity of Sonoziel. Their flavor of religious belief had become quite xenophobic after planetfall. Oddly enough, their nearly perfect world fueled this. Instead of relaxing in their good fortune, they eventually decided it was only their ideological purity that had allowed them to land there, and that outsiders’ sinful ways were a threat to their very existence.
Again, as every Alliance kid knows, their fanaticism eventually became the bloodiest war in Alliance history, leaving millions dead and entire planets devastated. One of those planets was Sonoziel itself, the once-beautiful planet left an uninhabitable, poisoned, radioactive rock with chasms down to the mantle in its shattered crust and a hemispherical crater where the Celestial Host made their last stand before self-destructing their stardrives.
After the Celestial Host War, A few things happened.
Open gaudy religious displays fell largely out of favor, especially displays of fanaticism and bigoted fanaticism of the “our religion says you’re icky, so even though you aren’t involved we’re going to treat you like garbage” variety. With Sonoziel and the Celestial Host as the go-to comparison for such behavior, social pressures keep most churches from getting too outrageous. If the local parish wants to do something harmless or beneficial like holding a parade or doing some charity work, most people smile and go along with it. When they show up at a funeral to push openly hostile religious propaganda on people who want nothing to do with them, that’s a different story entirely, and if violence erupts the police largely consider it self defense on the part of the people who weren’t inciting religious hatred over megaphones.
The Faithful were dragged out of the shadows. Before the War, they were a small, quiet cult going about their lives. Then they rescued the colonists at Bantumi and gave the Patrol a battlefield free of potential collateral damage, which allowed the Patrol to destroy the Umael in their first major victory. A major victory against what has so far been an unstoppable foe, aided by some weird religious group that just showed up to evacuate refugees because it was the right thing to do? That is exactly the kind of thing any propaganda network will exploit. Doubly so when this group is so scrupulous nobody can find anything of note to hold against them and when someone finds out their neighbor is one of them the response is usually “ah, that explains it. Best neighbors we’ve ever had.”
While this had minimal effect on the Faithful themselves, it had a subtle effect on the Alliance at large. When it became admirable for people to use their beliefs to help their fellow people rather than practice “we’re right, you’re wrong, convert or be treated like second-class citizens,” many of the more liberal churches started shifting their practices to be more community-oriented than all about aggrandizement of their religion.
There was a shift away from large organized religions, especially openly evangelical ones. Pressuring people into conversion quickly became extremely distasteful after what the Celestial Host had done. This also led to more people questioning the religious beliefs they had been raised with and subsequently either changing their religion or dropping it altogether. Combined with a centuries-long trend of general skepticism, this has led to the Alliance having a greater proportion of atheists than almost any other state in human history.
Some of Earth’s religions have survived the centuries, albeit not nearly as influential socially and politically as they once were. Christianity, Islam, Judaism, and Hinduism all have their adherents on multiple worlds, and some congregations have built some very impressive temples. Buddhism has emerged as a major religion in the Alliance, with its spread largely facilitated by its generally laid-back nature. After the abuses of the Celestial Host, it’s hard to get too honked over a religion that’s largely a philosophy of “be a decent human being and don’t do other people wrong.”
Non-traditional religious movements are common in the Alliance. Some of them resemble Earth’s neopagan religions, usually with a local twist. Others resemble other old Earth religions almost to the point of “dude, you just threw a new coat of paint on Taoism.”
Of course, the Alliance and unaffiliated worlds do have their share of nutcases. Full-fledged lunatic fringe cults appear on a regular basis and are usually put down pretty quickly once some fanatic decides their god really wants them to burn down the capitol building or sacrifice sex workers. In most cases it doesn’t even get that far. The kind of people attracted to cults like these aren’t exactly top-shelf humanity, and they always start bragging about their membership and how much better it makes them than everyone else. That attracts all the right kind of attention from the authorities, and Alliance surveillance technology can bring things to an end pretty quickly.
A few non-Alliance worlds were founded as religious enclaves. Visitors are advised to learn as much as possible about local customs before entering the system or especially making planetfall. Because they’re outside Alliance jurisdiction, visitors who find themselves on the wrong side of a bizarre local law will have little if any recourse available.